diff --git a/doc/userguide/capture-hardware/pcap-file.rst b/doc/userguide/capture-hardware/pcap-file.rst
index f87d259b74..d5ed628dde 100644
--- a/doc/userguide/capture-hardware/pcap-file.rst
+++ b/doc/userguide/capture-hardware/pcap-file.rst
@@ -15,6 +15,8 @@ Configuration
     checksum-checks: auto
     # buffer-size: 128 KiB
     # tenant-id: none
+    # Applies to file and directory. Options: false (no deletion), true (always delete),
+    #   "non-alerts" (delete only files with no alerts)
     # delete-when-done: false
     # recursive: false
     # continuous: false
@@ -85,9 +87,22 @@ Other options
 
 **delete-when-done**
 
-- If ``true``, Suricata deletes the PCAP file after processing.
-- The command-line option is
-  :ref:`--pcap-file-delete <cmdline-option-pcap-file-delete>`
+Controls when PCAP files are deleted after processing. Three values are supported:
+
+- ``false`` (default): Files are never deleted
+- ``true``: Files are always deleted after processing
+- ``"non-alerts"``: Files are deleted only if they didn't generate any alerts
+
+.. note::
+
+   The command-line option :ref:`--pcap-file-delete <cmdline-option-pcap-file-delete>`
+   overrides this configuration and forces "always delete" mode (``true``).
+
+.. warning::
+
+   When using ``"non-alerts"`` mode, file deletion is deferred until thread
+   cleanup to ensure alert counts are finalized. This may delay deletion
+   compared to other modes.
 
 **BPF filter**
 
diff --git a/doc/userguide/partials/options.rst b/doc/userguide/partials/options.rst
index 170677bff2..c11992e516 100644
--- a/doc/userguide/partials/options.rst
+++ b/doc/userguide/partials/options.rst
@@ -80,10 +80,23 @@
 
 .. option:: --pcap-file-delete
 
-   Used with the -r option to indicate that the mode should delete pcap files
-   after they have been processed. This is useful with pcap-file-continuous to
-   continuously feed files to a directory and have them cleaned up when done. If
-   this option is not set, pcap files will not be deleted after processing.
+   Used with the -r option to force deletion of pcap files after they have been
+   processed. This is useful with pcap-file-continuous to continuously feed files
+   to a directory and have them cleaned up when done.
+
+   **command-line vs Configuration**: This command-line option overrides the
+   ``pcap-file.delete-when-done`` configuration option in ``suricata.yaml`` and
+   forces "always delete" mode (equivalent to ``delete-when-done: true``).
+
+   **For more control**, use the ``pcap-file.delete-when-done`` configuration
+   option instead, which supports three values:
+
+   - ``false`` (default): No files are deleted
+   - ``true``: All files are deleted after processing
+   - ``"non-alerts"``: Only files that generated no alerts are deleted
+
+   If neither ``--pcap-file-delete`` nor ``delete-when-done`` is configured,
+   pcap files will not be deleted after processing.
 
 .. _cmdline-option-pcap-file-buffer-size:
 
diff --git a/src/Makefile.am b/src/Makefile.am
index f170992c6e..161061a2c1 100755
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -51,6 +51,7 @@ noinst_HEADERS = \
 	app-layer.h \
 	bindgen.h \
 	build-info.h \
+	capture-hooks.h \
 	conf-yaml-loader.h \
 	conf.h \
 	counters.h \
@@ -636,6 +637,7 @@ libsuricata_c_a_SOURCES = \
 	app-layer-ssl.c \
 	app-layer-tftp.c \
 	app-layer.c \
+	capture-hooks.c \
 	conf-yaml-loader.c \
 	conf.c \
 	counters.c \
diff --git a/src/capture-hooks.c b/src/capture-hooks.c
new file mode 100644
index 0000000000..92c8c69144
--- /dev/null
+++ b/src/capture-hooks.c
@@ -0,0 +1,65 @@
+/* Copyright (C) 2007-2026 Open Information Security Foundation
+ *
+ * You can copy, redistribute or modify this Program under the terms of
+ * the GNU General Public License version 2 as published by the Free
+ * Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * version 2 along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+/**
+ * \file
+ * Lightweight indirection layer for capture-related callbacks.
+ *
+ * This module lets the capture implementation register small hooks that the
+ * generic engine can invoke without hard dependencies. Two hooks are used:
+ * - on-alerts: invoked when a packet produced alerts so capture can update
+ *   per-input stats (e.g., deciding if a pcap should be deleted or kept).
+ * - on-pseudo-created: invoked when the engine creates pseudo packets (e.g.,
+ *   flow timeout or shutdown flush). This allows capture to retain references
+ *   or track alert outcomes tied to those pseudo packets.
+ */
+
+#include "suricata-common.h"
+#include "capture-hooks.h"
+
+static CaptureOnPacketWithAlertsHook g_on_alerts_hook = NULL;
+static CaptureOnPseudoPacketCreatedHook g_on_pseudo_created_hook = NULL;
+
+void CaptureHooksSet(
+        CaptureOnPacketWithAlertsHook OnAlerts, CaptureOnPseudoPacketCreatedHook OnPseudoCreated)
+{
+    /* Allow re-setting the same hooks (e.g. during pcap file reload), but BUG_ON
+     * if overwriting with different ones without clearing. */
+    if (g_on_alerts_hook != NULL) {
+        BUG_ON(g_on_alerts_hook != OnAlerts);
+    }
+    if (g_on_pseudo_created_hook != NULL) {
+        BUG_ON(g_on_pseudo_created_hook != OnPseudoCreated);
+    }
+
+    g_on_alerts_hook = OnAlerts;
+    g_on_pseudo_created_hook = OnPseudoCreated;
+}
+
+void CaptureHooksOnPacketWithAlerts(const Packet *p)
+{
+    if (g_on_alerts_hook != NULL) {
+        g_on_alerts_hook(p);
+    }
+}
+
+void CaptureHooksOnPseudoPacketCreated(Packet *p)
+{
+    if (g_on_pseudo_created_hook != NULL) {
+        g_on_pseudo_created_hook(p);
+    }
+}
diff --git a/src/capture-hooks.h b/src/capture-hooks.h
new file mode 100644
index 0000000000..350912a48a
--- /dev/null
+++ b/src/capture-hooks.h
@@ -0,0 +1,43 @@
+/* Copyright (C) 2007-2026 Open Information Security Foundation
+ *
+ * You can copy, redistribute or modify this Program under the terms of
+ * the GNU General Public License version 2 as published by the Free
+ * Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * version 2 along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+/**
+ * \file capture-hooks.h
+ * Small hook interface for capture modules to react to events in the
+ * generic engine without creating circular dependencies.
+ */
+
+#ifndef SURICATA_CAPTURE_HOOKS_H
+#define SURICATA_CAPTURE_HOOKS_H
+
+#include "suricata-common.h"
+
+struct Packet_;
+typedef struct Packet_ Packet;
+
+typedef void (*CaptureOnPacketWithAlertsHook)(const Packet *p);
+typedef void (*CaptureOnPseudoPacketCreatedHook)(Packet *p);
+
+/* Register/clear hooks (called by capture implementations) */
+void CaptureHooksSet(
+        CaptureOnPacketWithAlertsHook OnAlerts, CaptureOnPseudoPacketCreatedHook OnPseudoCreated);
+
+/* Invoke hooks (called from generic code, safe if unset) */
+void CaptureHooksOnPacketWithAlerts(const Packet *p);
+void CaptureHooksOnPseudoPacketCreated(Packet *p);
+
+#endif /* SURICATA_CAPTURE_HOOKS_H */
diff --git a/src/detect-engine-alert.c b/src/detect-engine-alert.c
index 4b2466d899..15929a8eb3 100644
--- a/src/detect-engine-alert.c
+++ b/src/detect-engine-alert.c
@@ -37,6 +37,7 @@
 #include "util-validate.h"
 
 #include "action-globals.h"
+#include "capture-hooks.h"
 
 /** tag signature we use for tag alerts */
 static Signature g_tag_signature;
@@ -582,6 +583,12 @@ static inline void PacketAlertFinalizeProcessQueue(
             p->flags |= PKT_FIRST_ALERTS;
         }
     }
+
+    /* Notify capture layer about packets with real alerts (not pass-only),
+     * so capture impl can update per-capture context (e.g. pcap-file alert counts). */
+    if (alerted) {
+        CaptureHooksOnPacketWithAlerts(p);
+    }
 }
 
 /**
diff --git a/src/runmode-unittests.c b/src/runmode-unittests.c
index 11565c0d75..c749315aab 100644
--- a/src/runmode-unittests.c
+++ b/src/runmode-unittests.c
@@ -116,6 +116,7 @@
 #include "decode-vntag.h"
 #include "decode-vxlan.h"
 #include "decode-pppoe.h"
+#include "source-pcap-file-helper.h"
 
 #include "output-json-stats.h"
 
@@ -212,6 +213,7 @@ static void RegisterUnittests(void)
     StreamingBufferRegisterTests();
     MacSetRegisterTests();
     FlowRateRegisterTests();
+    SourcePcapFileHelperRegisterTests();
 #ifdef OS_WIN32
     Win32SyscallRegisterTests();
 #endif
diff --git a/src/source-pcap-file-helper.c b/src/source-pcap-file-helper.c
index 8283ce9e85..0f3aac98f3 100644
--- a/src/source-pcap-file-helper.c
+++ b/src/source-pcap-file-helper.c
@@ -28,34 +28,77 @@
 #include "util-datalink.h"
 #include "util-checksum.h"
 #include "util-profiling.h"
-#include "source-pcap-file.h"
 #include "util-exception-policy.h"
+#include "conf-yaml-loader.h"
+#include "capture-hooks.h"
+#include "threads.h"
 
 extern uint32_t max_pending_packets;
 extern PcapFileGlobalVars pcap_g;
 
+static PcapFileFileVars *pcap_current_pfv = NULL;
+
 static void PcapFileCallbackLoop(char *user, struct pcap_pkthdr *h, u_char *pkt);
 
+static void PcapFileReleasePacket(Packet *p)
+{
+    PcapFileFileVars *pfv = p->pcap_v.pfv;
+    if (pfv != NULL) {
+        PcapFileFinalizePacket(pfv);
+    }
+
+    PacketFreeOrRelease(p);
+}
+
+void PcapFileReleasePseudoPacket(Packet *p)
+{
+    PcapFileFileVars *pfv = p->pcap_v.pfv;
+    /* Alerts are counted in PacketAlertFinalize via PcapFileAddAlertCount, so
+     * avoid double-counting here. Decrement refcount if we held one. */
+    if (pfv != NULL) {
+        uint32_t prev = SC_ATOMIC_SUB(pfv->ref_cnt, 1);
+        if (prev == 1 && pfv->cleanup_requested) {
+            CleanupPcapFileFileVars(pfv);
+        }
+    }
+    PacketFreeOrRelease(p);
+}
+
 void CleanupPcapFileFileVars(PcapFileFileVars *pfv)
 {
-    if (pfv != NULL) {
-        if (pfv->pcap_handle != NULL) {
-            pcap_close(pfv->pcap_handle);
-            pfv->pcap_handle = NULL;
-        }
-        if (pfv->filename != NULL) {
-            if (pfv->shared != NULL && pfv->shared->should_delete) {
-                SCLogDebug("Deleting pcap file %s", pfv->filename);
-                if (unlink(pfv->filename) != 0) {
-                    SCLogWarning("Failed to delete %s: %s", pfv->filename, strerror(errno));
-                }
-            }
-            SCFree(pfv->filename);
-            pfv->filename = NULL;
-        }
-        pfv->shared = NULL;
-        SCFree(pfv);
+    if (pfv == NULL) {
+        return;
     }
+
+    /* If there are still packets in flight, defer ALL cleanup actions, including
+     * the deletion decision, until the last packet completes. */
+    if (SC_ATOMIC_GET(pfv->ref_cnt) != 0) {
+        pfv->cleanup_requested = true;
+        return;
+    }
+
+    /* No packets in flight anymore: it's now safe to close, decide, and delete. */
+    if (pfv->pcap_handle != NULL) {
+        pcap_close(pfv->pcap_handle);
+        pfv->pcap_handle = NULL;
+    }
+
+    if (pfv->filename != NULL) {
+        if (PcapFileShouldDeletePcapFile(pfv)) {
+            SCLogDebug("Deleting pcap file %s", pfv->filename);
+            if (unlink(pfv->filename) != 0) {
+                SCLogWarning("Failed to delete %s: %s", pfv->filename, strerror(errno));
+            }
+        }
+        SCFree(pfv->filename);
+        pfv->filename = NULL;
+    }
+
+    pfv->shared = NULL;
+    if (pcap_current_pfv == pfv) {
+        pcap_current_pfv = NULL;
+    }
+    SCFree(pfv);
 }
 
 void PcapFileCallbackLoop(char *user, struct pcap_pkthdr *h, u_char *pkt)
@@ -74,6 +117,10 @@ void PcapFileCallbackLoop(char *user, struct pcap_pkthdr *h, u_char *pkt)
     if (unlikely(p == NULL)) {
         SCReturn;
     }
+    SC_ATOMIC_ADD(ptv->ref_cnt, 1);
+    SCLogDebug("pcap-file: got packet, pfv=%p filename=%s ref_cnt now=%u p=%p", (void *)ptv,
+            ptv->filename, SC_ATOMIC_GET(ptv->ref_cnt), (void *)p);
+
     PACKET_PROFILING_TMM_START(p, TMM_RECEIVEPCAPFILE);
 
     PKT_SET_SRC(p, PKT_SRC_WIRE);
@@ -83,9 +130,12 @@ void PcapFileCallbackLoop(char *user, struct pcap_pkthdr *h, u_char *pkt)
     p->pcap_v.pcap_cnt = ++pcap_g.cnt;
 
     p->pcap_v.tenant_id = ptv->shared->tenant_id;
+    p->pcap_v.pfv = ptv;
     ptv->shared->pkts++;
     ptv->shared->bytes += h->caplen;
 
+    p->ReleasePacket = PcapFileReleasePacket;
+
     if (unlikely(PacketCopyData(p, pkt, h->caplen))) {
         TmqhOutputPacketpool(ptv->shared->tv, p);
         PACKET_PROFILING_TMM_END(p, TMM_RECEIVEPCAPFILE);
@@ -120,6 +170,16 @@ const char *PcapFileGetFilename(void)
     return pcap_filename;
 }
 
+void PcapFileSetCurrentPfv(PcapFileFileVars *pfv)
+{
+    pcap_current_pfv = pfv;
+}
+
+PcapFileFileVars *PcapFileGetCurrentPfv(void)
+{
+    return pcap_current_pfv;
+}
+
 /**
  *  \brief Main PCAP file reading Loop function
  */
@@ -127,6 +187,7 @@ TmEcode PcapFileDispatch(PcapFileFileVars *ptv)
 {
     SCEnter();
 
+    PcapFileSetCurrentPfv(ptv);
     /* initialize all the thread's initial timestamp */
     if (likely(ptv->first_pkt_hdr != NULL)) {
         TmThreadsInitThreadsTimestamp(SCTIME_FROM_TIMEVAL(&ptv->first_pkt_ts));
@@ -236,6 +297,14 @@ TmEcode InitPcapFile(PcapFileFileVars *pfv)
         pcap_freecode(&pfv->filter);
     }
 
+    SC_ATOMIC_INIT(pfv->alerts_count);
+    SC_ATOMIC_SET(pfv->alerts_count, 0);
+
+    SC_ATOMIC_INIT(pfv->ref_cnt);
+    SC_ATOMIC_SET(pfv->ref_cnt, 0);
+
+    pfv->cleanup_requested = false;
+
     pfv->datalink = pcap_datalink(pfv->pcap_handle);
     SCLogDebug("datalink %" PRId32 "", pfv->datalink);
     DatalinkSetGlobalType(pfv->datalink);
@@ -285,3 +354,687 @@ TmEcode ValidateLinkType(int datalink, DecoderFunc *DecoderFn)
 
     SCReturnInt(TM_ECODE_OK);
 }
+
+bool PcapFileShouldDeletePcapFile(PcapFileFileVars *pfv)
+{
+    if (pfv == NULL || pfv->shared == NULL) {
+        return false;
+    }
+
+    if (pfv->shared->delete_mode == PCAP_FILE_DELETE_NONE) {
+        return false;
+    }
+
+    if (pfv->shared->delete_mode == PCAP_FILE_DELETE_ALWAYS) {
+        return true;
+    }
+
+    /* PCAP_FILE_DELETE_NON_ALERTS mode */
+    uint64_t file_alerts = SC_ATOMIC_GET(pfv->alerts_count);
+
+    if (file_alerts != 0) {
+        SCLogDebug("Skipping deletion of %s due to %" PRIu64 " alert(s) generated.", pfv->filename,
+                file_alerts);
+        return false;
+    }
+
+    SCLogDebug("pcap-file: will delete %s (no alerts counted)", pfv->filename);
+
+    return true;
+}
+
+void PcapFileFinalizePacket(PcapFileFileVars *pfv)
+{
+    if (pfv != NULL) {
+        /* decrease ref count as packet is done */
+        uint32_t prev = SC_ATOMIC_SUB(pfv->ref_cnt, 1);
+        SCLogDebug("pcap-file: packet done pfv=%p filename=%s ref_cnt was=%u now=%u", (void *)pfv,
+                pfv->filename, prev, prev - 1);
+        if (prev == 1) {
+            if (pfv->cleanup_requested) {
+                CleanupPcapFileFileVars(pfv);
+            }
+        }
+    }
+}
+
+void PcapFileAddAlertCount(PcapFileFileVars *pfv, uint16_t alert_count)
+{
+    if (pfv != NULL && alert_count > 0) {
+        SC_ATOMIC_ADD(pfv->alerts_count, alert_count);
+    }
+}
+
+static void PcapCaptureOnPacketWithAlerts(const Packet *p)
+{
+    PcapFileFileVars *pfv = p->pcap_v.pfv;
+    if (pfv == NULL) {
+        pfv = PcapFileGetCurrentPfv();
+    }
+    if (pfv != NULL) {
+        /* alerts.cnt is uint16_t; count alerts for delete-on-non-alerts logic */
+        PcapFileAddAlertCount(pfv, p->alerts.cnt);
+    }
+}
+
+static void PcapCaptureOnPseudoPacketCreated(Packet *p)
+{
+    /* For pseudo packets created by generic layers, associate with current pfv
+     * and ensure refcount held so deletion defers. */
+    if (p->pcap_v.pfv == NULL) {
+        PcapFileFileVars *pfv = PcapFileGetCurrentPfv();
+        if (pfv != NULL) {
+            p->pcap_v.pfv = pfv;
+            p->ReleasePacket = PcapFileReleasePseudoPacket;
+            SC_ATOMIC_ADD(pfv->ref_cnt, 1);
+        }
+    }
+}
+
+void PcapFileInstallCaptureHooks(void)
+{
+    CaptureHooksSet(PcapCaptureOnPacketWithAlerts, PcapCaptureOnPseudoPacketCreated);
+}
+
+PcapFileDeleteMode PcapFileParseDeleteMode(void)
+{
+    PcapFileDeleteMode delete_mode = PCAP_FILE_DELETE_NONE;
+    const char *delete_when_done_str = NULL;
+
+    if (SCConfGet("pcap-file.delete-when-done", &delete_when_done_str) == 1) {
+        if (strcmp(delete_when_done_str, "non-alerts") == 0) {
+            delete_mode = PCAP_FILE_DELETE_NON_ALERTS;
+        } else {
+            int delete_always = 0;
+            if (SCConfGetBool("pcap-file.delete-when-done", &delete_always) == 1) {
+                if (delete_always == 1) {
+                    delete_mode = PCAP_FILE_DELETE_ALWAYS;
+                }
+            }
+        }
+    }
+
+    return delete_mode;
+}
+
+#ifdef UNITTESTS
+#include "util-unittest-helper.h"
+/**
+ * \test Tests that the PcapFileShouldDeletePcapFile function correctly applies the
+ * delete mode configuration.
+ */
+static int SourcePcapFileHelperTest01(void)
+{
+    PcapFileSharedVars shared;
+    memset(&shared, 0, sizeof(shared));
+    shared.delete_mode = PCAP_FILE_DELETE_ALWAYS;
+
+    PcapFileFileVars pfv;
+    memset(&pfv, 0, sizeof(pfv));
+    pfv.shared = &shared;
+    pfv.filename = SCStrdup("test.pcap");
+    SC_ATOMIC_INIT(pfv.alerts_count);
+    SC_ATOMIC_SET(pfv.alerts_count, 0);
+
+    /* Test case 1: Always delete mode */
+    int result1 = PcapFileShouldDeletePcapFile(&pfv);
+    FAIL_IF_NOT(result1);
+
+    /* Test case 2: Non-alerts mode with no alerts */
+    shared.delete_mode = PCAP_FILE_DELETE_NON_ALERTS;
+    int result2 = PcapFileShouldDeletePcapFile(&pfv);
+    FAIL_IF_NOT(result2);
+
+    /* Test case 3: Non-alerts mode with alerts */
+    SC_ATOMIC_ADD(pfv.alerts_count, 1);
+    int result3 = PcapFileShouldDeletePcapFile(&pfv);
+    FAIL_IF(result3);
+
+    /* Test case 4: Always delete mode with alerts */
+    shared.delete_mode = PCAP_FILE_DELETE_ALWAYS;
+    int result4 = PcapFileShouldDeletePcapFile(&pfv);
+    FAIL_IF_NOT(result4);
+
+    /* Test case 5: No delete mode */
+    shared.delete_mode = PCAP_FILE_DELETE_NONE;
+    int result5 = PcapFileShouldDeletePcapFile(&pfv);
+    FAIL_IF(result5);
+
+    SCFree(pfv.filename);
+
+    PASS;
+}
+
+/**
+ * \test Test PcapFileFinalizePacket function with reference counting
+ */
+static int SourcePcapFileHelperTest02(void)
+{
+    PcapFileFileVars pfv;
+    memset(&pfv, 0, sizeof(pfv));
+    SC_ATOMIC_INIT(pfv.alerts_count);
+    SC_ATOMIC_SET(pfv.alerts_count, 0);
+    SC_ATOMIC_INIT(pfv.ref_cnt);
+    SC_ATOMIC_SET(pfv.ref_cnt, 0);
+    pfv.cleanup_requested = false;
+
+    /* Test adding alerts with reference counting */
+    SC_ATOMIC_ADD(pfv.ref_cnt, 1); /* simulate packet in flight */
+    PcapFileAddAlertCount(&pfv, 5);
+    PcapFileFinalizePacket(&pfv);
+    uint64_t count = SC_ATOMIC_GET(pfv.alerts_count);
+    FAIL_IF_NOT(count == 5);
+    FAIL_IF_NOT(SC_ATOMIC_GET(pfv.ref_cnt) == 0); /* should be decremented */
+
+    /* Test adding more alerts */
+    SC_ATOMIC_ADD(pfv.ref_cnt, 1);
+    PcapFileAddAlertCount(&pfv, 3);
+    PcapFileFinalizePacket(&pfv);
+    count = SC_ATOMIC_GET(pfv.alerts_count);
+    FAIL_IF_NOT(count == 8);
+
+    /* Test with zero alerts (should not increment count) */
+    SC_ATOMIC_ADD(pfv.ref_cnt, 1);
+    PcapFileFinalizePacket(&pfv);
+    count = SC_ATOMIC_GET(pfv.alerts_count);
+    FAIL_IF_NOT(count == 8);
+
+    /* Test with NULL pfv (should not crash) */
+    PcapFileFinalizePacket(NULL);
+
+    PASS;
+}
+
+/* Mock for configuration testing */
+static int SetupYamlConf(const char *conf_string)
+{
+    SCConfCreateContextBackup();
+    SCConfInit();
+
+    return SCConfYamlLoadString(conf_string, strlen(conf_string));
+}
+
+static void CleanupYamlConf(void)
+{
+    SCConfDeInit();
+    SCConfRestoreContextBackup();
+}
+
+/**
+ * \test Test PcapFileParseDeleteMode with all configuration combinations
+ */
+static int SourcePcapFileHelperTest03(void)
+{
+    /* Test 1: No configuration (should default to NONE) */
+    SCConfCreateContextBackup();
+    SCConfInit();
+
+    PcapFileDeleteMode result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_NONE);
+
+    SCConfDeInit();
+    SCConfRestoreContextBackup();
+
+    /* Test 2: "false" configuration */
+    const char *conf_false = "%YAML 1.1\n"
+                             "---\n"
+                             "pcap-file:\n"
+                             "  delete-when-done: false\n";
+
+    SetupYamlConf(conf_false);
+    result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_NONE);
+    CleanupYamlConf();
+
+    /* Test 3: "true" configuration */
+    const char *conf_true = "%YAML 1.1\n"
+                            "---\n"
+                            "pcap-file:\n"
+                            "  delete-when-done: true\n";
+
+    SetupYamlConf(conf_true);
+    result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_ALWAYS);
+    CleanupYamlConf();
+
+    /* Test 4: "non-alerts" configuration */
+    const char *conf_non_alerts = "%YAML 1.1\n"
+                                  "---\n"
+                                  "pcap-file:\n"
+                                  "  delete-when-done: \"non-alerts\"\n";
+
+    SetupYamlConf(conf_non_alerts);
+    result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_NON_ALERTS);
+    CleanupYamlConf();
+
+    /* Test 5: Invalid configuration (should default to NONE) */
+    const char *conf_invalid = "%YAML 1.1\n"
+                               "---\n"
+                               "pcap-file:\n"
+                               "  delete-when-done: \"invalid-value\"\n";
+
+    SetupYamlConf(conf_invalid);
+    result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_NONE);
+    CleanupYamlConf();
+
+    PASS;
+}
+
+/**
+ * \test pfv is NULL.
+ */
+static int SourcePcapFileHelperTest04(void)
+{
+    int rc = PcapFileShouldDeletePcapFile(NULL);
+    FAIL_IF(rc);
+    PASS;
+}
+
+/**
+ * \test pfv->shared is NULL.
+ */
+static int SourcePcapFileHelperTest05(void)
+{
+    PcapFileFileVars pfv;
+    memset(&pfv, 0, sizeof(pfv));
+
+    int rc = PcapFileShouldDeletePcapFile(&pfv);
+    FAIL_IF(rc);
+    PASS;
+}
+
+/**
+ * \test Test cleanup with reference counting and deferred deletion
+ */
+static int SourcePcapFileHelperTest06(void)
+{
+    PcapFileFileVars pfv;
+    memset(&pfv, 0, sizeof(pfv));
+    SC_ATOMIC_INIT(pfv.alerts_count);
+    SC_ATOMIC_SET(pfv.alerts_count, 0);
+    SC_ATOMIC_INIT(pfv.ref_cnt);
+    SC_ATOMIC_SET(pfv.ref_cnt, 2); /* simulate 2 packets in flight */
+    pfv.cleanup_requested = false;
+
+    /* Simulate first packet completion - should not cleanup yet */
+    SC_ATOMIC_SUB(pfv.ref_cnt, 1);
+    FAIL_IF_NOT(SC_ATOMIC_GET(pfv.ref_cnt) == 1);
+
+    /* Request cleanup while packets are still in flight */
+    pfv.cleanup_requested = true;
+
+    /* Simulate second packet completion - should trigger cleanup */
+    if (SC_ATOMIC_SUB(pfv.ref_cnt, 1) == 1) {
+        FAIL_IF_NOT(pfv.cleanup_requested); /* cleanup should have been requested */
+        /* In real code, CleanupPcapFileFileVars would be called here */
+    }
+
+    PASS;
+}
+
+/**
+ * \test Test edge cases and error conditions
+ */
+static int SourcePcapFileHelperTest07(void)
+{
+    /* Test 1: PcapFileShouldDeletePcapFile with very high alert count */
+    PcapFileSharedVars shared;
+    memset(&shared, 0, sizeof(shared));
+    shared.delete_mode = PCAP_FILE_DELETE_NON_ALERTS;
+
+    PcapFileFileVars pfv;
+    memset(&pfv, 0, sizeof(pfv));
+    pfv.shared = &shared;
+    pfv.filename = SCStrdup("test.pcap");
+    SC_ATOMIC_INIT(pfv.alerts_count);
+    SC_ATOMIC_SET(pfv.alerts_count, UINT64_MAX); /* max value */
+
+    int result = PcapFileShouldDeletePcapFile(&pfv);
+    FAIL_IF(result); /* should not delete with max alerts */
+
+    /* Test 2: PcapFileFinalizePacket with max alert count */
+    SC_ATOMIC_INIT(pfv.ref_cnt);
+    SC_ATOMIC_ADD(pfv.ref_cnt, 1);
+    PcapFileAddAlertCount(&pfv, UINT16_MAX); /* max uint16_t */
+    PcapFileFinalizePacket(&pfv);
+    /* Should not overflow or crash */
+
+    SCFree(pfv.filename);
+    PASS;
+}
+
+/**
+ * \test Test command-line --pcap-file-delete override behavior
+ */
+static int SourcePcapFileHelperTest08(void)
+{
+    /* Test 1: Command line overrides YAML "false" */
+    const char *conf_false = "%YAML 1.1\n"
+                             "---\n"
+                             "pcap-file:\n"
+                             "  delete-when-done: false\n";
+
+    SetupYamlConf(conf_false);
+
+    /* Simulate --pcap-file-delete command line option */
+    int set_result = SCConfSetFinal("pcap-file.delete-when-done", "true");
+    FAIL_IF_NOT(set_result == 1);
+
+    PcapFileDeleteMode result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_ALWAYS); /* Should override YAML false */
+    CleanupYamlConf();
+
+    /* Test 2: Command line overrides YAML "non-alerts" */
+    const char *conf_non_alerts = "%YAML 1.1\n"
+                                  "---\n"
+                                  "pcap-file:\n"
+                                  "  delete-when-done: \"non-alerts\"\n";
+
+    SetupYamlConf(conf_non_alerts);
+
+    /* Simulate --pcap-file-delete command line option */
+    set_result = SCConfSetFinal("pcap-file.delete-when-done", "true");
+    FAIL_IF_NOT(set_result == 1);
+
+    result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_ALWAYS); /* Should override YAML "non-alerts" */
+    CleanupYamlConf();
+
+    /* Test 3: Command line overrides no YAML config */
+    SCConfCreateContextBackup();
+    SCConfInit();
+
+    /* Simulate --pcap-file-delete command line option with no YAML config */
+    set_result = SCConfSetFinal("pcap-file.delete-when-done", "true");
+    FAIL_IF_NOT(set_result == 1);
+
+    result = PcapFileParseDeleteMode();
+    FAIL_IF_NOT(result == PCAP_FILE_DELETE_ALWAYS); /* Should set to always delete */
+
+    SCConfDeInit();
+    SCConfRestoreContextBackup();
+
+    PASS;
+}
+
+/**
+ * \test Test that cleanup defers while packets are in flight and that a file
+ * with alerts is not deleted in NON_ALERTS mode.
+ */
+static int SourcePcapFileHelperTest09(void)
+{
+    PcapFileSharedVars *shared = SCCalloc(1, sizeof(*shared));
+    FAIL_IF_NULL(shared);
+    shared->delete_mode = PCAP_FILE_DELETE_NON_ALERTS;
+
+    PcapFileFileVars *pfv = SCCalloc(1, sizeof(*pfv));
+    FAIL_IF_NULL(pfv);
+    pfv->shared = shared;
+    pfv->filename = SCStrdup("unit_del_test.pcap");
+    FAIL_IF_NULL(pfv->filename);
+
+    SC_ATOMIC_INIT(pfv->alerts_count);
+    SC_ATOMIC_SET(pfv->alerts_count, 0);
+    SC_ATOMIC_INIT(pfv->ref_cnt);
+    SC_ATOMIC_SET(pfv->ref_cnt, 2); /* two packets in flight */
+    pfv->cleanup_requested = false;
+
+    /* Request cleanup while packets still in flight: should defer. */
+    CleanupPcapFileFileVars(pfv);
+    FAIL_IF_NOT(pfv->cleanup_requested);
+    FAIL_IF_NULL(pfv->filename); /* not freed yet */
+
+    /* First packet completes and generates an alert. */
+    PcapFileAddAlertCount(pfv, 1);
+    PcapFileFinalizePacket(pfv);
+    FAIL_IF_NOT(SC_ATOMIC_GET(pfv->alerts_count) == 1);
+
+    /* Second (last) packet completes: triggers final cleanup. */
+    PcapFileFinalizePacket(pfv);
+
+    /* pfv memory is freed at this point; only free shared. */
+    SCFree(shared);
+
+    PASS;
+}
+
+/**
+ * \test Cover unlink-on-ALWAYS branch (ref_cnt == 0) and deferred deletion when ref_cnt > 0
+ */
+static int SourcePcapFileHelperTest10(void)
+{
+    /* Create a temporary file that we expect to be deleted. */
+    const char *tmpname = "suri_ut_delete_always.pcap";
+    const uint8_t dummy[] = { 0x00 };
+    int rc = TestHelperBufferToFile(tmpname, dummy, sizeof(dummy));
+    FAIL_IF_NOT(rc >= 0);
+
+    /* Case 1: delete ALWAYS with no packets in flight -> file unlinked immediately */
+    PcapFileSharedVars *shared1 = SCCalloc(1, sizeof(*shared1));
+    FAIL_IF_NULL(shared1);
+    shared1->delete_mode = PCAP_FILE_DELETE_ALWAYS;
+
+    PcapFileFileVars *pfv1 = SCCalloc(1, sizeof(*pfv1));
+    FAIL_IF_NULL(pfv1);
+    pfv1->shared = shared1;
+    pfv1->filename = SCStrdup(tmpname);
+    FAIL_IF_NULL(pfv1->filename);
+
+    SC_ATOMIC_INIT(pfv1->alerts_count);
+    SC_ATOMIC_SET(pfv1->alerts_count, 0);
+    SC_ATOMIC_INIT(pfv1->ref_cnt);
+    SC_ATOMIC_SET(pfv1->ref_cnt, 0);
+
+    /* Provide a closable handle to cover close path. */
+    pfv1->pcap_handle = pcap_open_dead(DLT_EN10MB, 65535);
+    FAIL_IF_NULL(pfv1->pcap_handle);
+
+    CleanupPcapFileFileVars(pfv1);
+
+    /* File should be gone. */
+    FILE *f = fopen(tmpname, "rb");
+    FAIL_IF_NOT_NULL(f);
+    if (f != NULL)
+        fclose(f);
+
+    /* Case 2: delete ALWAYS but ref_cnt > 0 -> defer until finalize. */
+    /* Recreate the file. */
+    rc = TestHelperBufferToFile(tmpname, dummy, sizeof(dummy));
+    FAIL_IF_NOT(rc >= 0);
+
+    PcapFileSharedVars *shared2 = SCCalloc(1, sizeof(*shared2));
+    FAIL_IF_NULL(shared2);
+    shared2->delete_mode = PCAP_FILE_DELETE_ALWAYS;
+
+    PcapFileFileVars *pfv2 = SCCalloc(1, sizeof(*pfv2));
+    FAIL_IF_NULL(pfv2);
+    pfv2->shared = shared2;
+    pfv2->filename = SCStrdup(tmpname);
+    FAIL_IF_NULL(pfv2->filename);
+
+    SC_ATOMIC_INIT(pfv2->alerts_count);
+    SC_ATOMIC_SET(pfv2->alerts_count, 0);
+    SC_ATOMIC_INIT(pfv2->ref_cnt);
+    SC_ATOMIC_SET(pfv2->ref_cnt, 1);
+    pfv2->pcap_handle = pcap_open_dead(DLT_EN10MB, 65535);
+    FAIL_IF_NULL(pfv2->pcap_handle);
+
+    CleanupPcapFileFileVars(pfv2);
+
+    /* Still exists now because deletion should be deferred. */
+    f = fopen(tmpname, "rb");
+    FAIL_IF_NULL(f);
+    if (f != NULL)
+        fclose(f);
+
+    /* Finalize the last packet which should trigger final cleanup & unlink. */
+    PcapFileFinalizePacket(pfv2);
+
+    /* Now the file should be gone. */
+    f = fopen(tmpname, "rb");
+    FAIL_IF_NOT_NULL(f);
+    if (f != NULL)
+        fclose(f);
+
+    SCFree(shared1);
+    SCFree(shared2);
+
+    PASS;
+}
+
+/**
+ * \test Test PcapFileReleasePseudoPacket refcount decrement without cleanup
+ */
+static int SourcePcapFileHelperTest11(void)
+{
+    /* Setup pfv with ref_cnt=2 so release does not trigger cleanup */
+    PcapFileFileVars pfv;
+    memset(&pfv, 0, sizeof(pfv));
+    SC_ATOMIC_INIT(pfv.ref_cnt);
+    SC_ATOMIC_SET(pfv.ref_cnt, 2);
+    pfv.cleanup_requested = false;
+
+    /* Allocate a packet from the pool to allow safe release */
+    Packet *p = PacketGetFromAlloc();
+    FAIL_IF_NULL(p);
+    p->pcap_v.pfv = &pfv;
+
+    /* Call release and ensure ref count decremented by 1 */
+    PcapFileReleasePseudoPacket(p);
+    FAIL_IF_NOT(SC_ATOMIC_GET(pfv.ref_cnt) == 1);
+
+    PASS;
+}
+
+/**
+ * \test Test adding alert count and that cleanup after refcnt reaches zero
+ *       does not delete when alerts exist in NON_ALERTS mode.
+ */
+static int SourcePcapFileHelperTest12(void)
+{
+    PcapFileSharedVars shared;
+    memset(&shared, 0, sizeof(shared));
+    shared.delete_mode = PCAP_FILE_DELETE_NON_ALERTS;
+
+    PcapFileFileVars *pfv = SCCalloc(1, sizeof(*pfv));
+    FAIL_IF_NULL(pfv);
+    pfv->shared = &shared;
+    pfv->filename = SCStrdup("ut_non_alerts.pcap");
+    FAIL_IF_NULL(pfv->filename);
+
+    SC_ATOMIC_INIT(pfv->alerts_count);
+    SC_ATOMIC_SET(pfv->alerts_count, 0);
+    SC_ATOMIC_INIT(pfv->ref_cnt);
+    SC_ATOMIC_SET(pfv->ref_cnt, 1);
+    pfv->cleanup_requested = true;
+
+    /* Simulate pseudo alert */
+    PcapFileAddAlertCount(pfv, 2);
+    FAIL_IF_NOT(SC_ATOMIC_GET(pfv->alerts_count) == 2);
+
+    /* Simulate last ref release triggering cleanup; file shouldn't be deleted
+     * due to alerts > 0. We cannot check unlink here; rely on return value. */
+    if (SC_ATOMIC_SUB(pfv->ref_cnt, 1) == 1) {
+        CleanupPcapFileFileVars(pfv);
+    }
+    /* Success if no crash. */
+    PASS;
+}
+
+/**
+ * \test Test global current pfv pointer lifecycle
+ */
+static int SourcePcapFileHelperTest13(void)
+{
+    PcapFileFileVars *pfv = SCCalloc(1, sizeof(*pfv));
+    FAIL_IF_NULL(pfv);
+    pfv->filename = SCStrdup("ut_global_clear.pcap");
+    FAIL_IF_NULL(pfv->filename);
+
+    PcapFileSetCurrentPfv(pfv);
+    FAIL_IF_NOT(PcapFileGetCurrentPfv() == pfv);
+
+    /* Cleanup should clear global reference when pointing to this pfv */
+    CleanupPcapFileFileVars(pfv);
+    /* Global accessor must be NULL after cleanup. */
+    FAIL_IF_NOT(PcapFileGetCurrentPfv() == NULL);
+    PASS;
+}
+
+/**
+ * \test Exercise unlink failure branch in CleanupPcapFileFileVars
+ */
+static int SourcePcapFileHelperTest14(void)
+{
+    PcapFileSharedVars shared;
+    memset(&shared, 0, sizeof(shared));
+    shared.delete_mode = PCAP_FILE_DELETE_ALWAYS;
+
+    PcapFileFileVars *pfv = SCCalloc(1, sizeof(*pfv));
+    FAIL_IF_NULL(pfv);
+    pfv->shared = &shared;
+    pfv->filename = SCStrdup("does-not-exist-ut.pcap");
+    FAIL_IF_NULL(pfv->filename);
+
+    SC_ATOMIC_INIT(pfv->ref_cnt);
+    SC_ATOMIC_SET(pfv->ref_cnt, 0);
+
+    /* Attempt cleanup; unlink should fail but must not crash */
+    CleanupPcapFileFileVars(pfv);
+    PASS;
+}
+
+/**
+ * \test Cover alerts hook fallback using current PFV
+ */
+static int SourcePcapFileHelperTest15(void)
+{
+    PcapFileInstallCaptureHooks();
+
+    PcapFileFileVars *pfv = SCCalloc(1, sizeof(*pfv));
+    FAIL_IF_NULL(pfv);
+    SC_ATOMIC_INIT(pfv->alerts_count);
+    SC_ATOMIC_SET(pfv->alerts_count, 0);
+
+    /* Set current PFV to exercise fallback path */
+    PcapFileSetCurrentPfv(pfv);
+
+    Packet *p = PacketGetFromAlloc();
+    FAIL_IF_NULL(p);
+    p->alerts.cnt = 3;    /* simulate 3 alerts */
+    p->pcap_v.pfv = NULL; /* force fallback */
+
+    /* Call hook: it should update pfv->alerts_count */
+    CaptureHooksOnPacketWithAlerts(p);
+    FAIL_IF_NOT(SC_ATOMIC_GET(pfv->alerts_count) == 3);
+
+    /* Cleanup */
+    PacketFreeOrRelease(p);
+    CleanupPcapFileFileVars(pfv);
+    PASS;
+}
+
+/**
+ * \brief Register unit tests for pcap file helper
+ */
+void SourcePcapFileHelperRegisterTests(void)
+{
+    UtRegisterTest("SourcePcapFileHelperTest01", SourcePcapFileHelperTest01);
+    UtRegisterTest("SourcePcapFileHelperTest02", SourcePcapFileHelperTest02);
+    UtRegisterTest("SourcePcapFileHelperTest03", SourcePcapFileHelperTest03);
+    UtRegisterTest("SourcePcapFileHelperTest04", SourcePcapFileHelperTest04);
+    UtRegisterTest("SourcePcapFileHelperTest05", SourcePcapFileHelperTest05);
+    UtRegisterTest("SourcePcapFileHelperTest06", SourcePcapFileHelperTest06);
+    UtRegisterTest("SourcePcapFileHelperTest07", SourcePcapFileHelperTest07);
+    UtRegisterTest("SourcePcapFileHelperTest08", SourcePcapFileHelperTest08);
+    UtRegisterTest("SourcePcapFileHelperTest09", SourcePcapFileHelperTest09);
+    UtRegisterTest("SourcePcapFileHelperTest10", SourcePcapFileHelperTest10);
+    UtRegisterTest("SourcePcapFileHelperTest11", SourcePcapFileHelperTest11);
+    UtRegisterTest("SourcePcapFileHelperTest12", SourcePcapFileHelperTest12);
+    UtRegisterTest("SourcePcapFileHelperTest13", SourcePcapFileHelperTest13);
+    UtRegisterTest("SourcePcapFileHelperTest14", SourcePcapFileHelperTest14);
+    UtRegisterTest("SourcePcapFileHelperTest15", SourcePcapFileHelperTest15);
+}
+#endif /* UNITTESTS */
diff --git a/src/source-pcap-file-helper.h b/src/source-pcap-file-helper.h
index 2de7d16cc3..7d59d4fc75 100644
--- a/src/source-pcap-file-helper.h
+++ b/src/source-pcap-file-helper.h
@@ -23,10 +23,17 @@
 
 #include "suricata-common.h"
 #include "tm-threads.h"
+#include "util-atomic.h"
 
 #ifndef SURICATA_SOURCE_PCAP_FILE_HELPER_H
 #define SURICATA_SOURCE_PCAP_FILE_HELPER_H
 
+typedef enum {
+    PCAP_FILE_DELETE_NONE = 0,
+    PCAP_FILE_DELETE_ALWAYS,
+    PCAP_FILE_DELETE_NON_ALERTS
+} PcapFileDeleteMode;
+
 typedef struct PcapFileGlobalVars_ {
     uint64_t cnt; /** packet counter */
     ChecksumValidationMode conf_checksum_mode;
@@ -46,7 +53,7 @@ typedef struct PcapFileSharedVars_
 
     struct timespec last_processed;
 
-    bool should_delete;
+    PcapFileDeleteMode delete_mode;
 
     ThreadVars *tv;
     TmSlot *slot;
@@ -76,6 +83,14 @@ typedef struct PcapFileFileVars_
 
     PcapFileSharedVars *shared;
 
+    SC_ATOMIC_DECLARE(uint64_t, alerts_count);
+    /* Reference count for outstanding users (e.g., pseudo packets created
+     * during shutdown/timeout handling). Ensures the per-file state is not
+     * cleaned up or the file deleted before all dependent processing that may
+     * still raise alerts has completed. */
+    SC_ATOMIC_DECLARE(uint32_t, ref_cnt);
+    bool cleanup_requested;
+
     /* fields used to get the first packet's timestamp early,
      * so it can be used to setup the time subsys. */
     const u_char *first_pkt_data;
@@ -121,4 +136,23 @@ TmEcode ValidateLinkType(int datalink, DecoderFunc *decoder);
 
 const char *PcapFileGetFilename(void);
 
+bool PcapFileShouldDeletePcapFile(PcapFileFileVars *pfv);
+
+void PcapFileFinalizePacket(PcapFileFileVars *pfv);
+
+PcapFileDeleteMode PcapFileParseDeleteMode(void);
+
+void PcapFileAddAlertCount(PcapFileFileVars *pfv, uint16_t alert_count);
+
+void PcapFileReleasePseudoPacket(Packet *p);
+
+void PcapFileSetCurrentPfv(PcapFileFileVars *pfv);
+PcapFileFileVars *PcapFileGetCurrentPfv(void);
+
+void PcapFileInstallCaptureHooks(void);
+
+#ifdef UNITTESTS
+void SourcePcapFileHelperRegisterTests(void);
+#endif
+
 #endif /* SURICATA_SOURCE_PCAP_FILE_HELPER_H */
diff --git a/src/source-pcap-file.c b/src/source-pcap-file.c
index 75252bc3bb..fd15b2036e 100644
--- a/src/source-pcap-file.c
+++ b/src/source-pcap-file.c
@@ -33,6 +33,7 @@
 #include "suricata.h"
 #include "conf.h"
 #include "util-misc.h"
+#include "capture-hooks.h"
 
 extern uint32_t max_pending_packets;
 PcapFileGlobalVars pcap_g;
@@ -148,6 +149,8 @@ void PcapFileGlobalInit(void)
     memset(&pcap_g, 0x00, sizeof(pcap_g));
     SC_ATOMIC_INIT(pcap_g.invalid_checksums);
 
+    PcapFileInstallCaptureHooks();
+
 #if defined(HAVE_SETVBUF) && defined(OS_LINUX)
     pcap_g.read_buffer_size = PCAP_FILE_BUFFER_SIZE_DEFAULT;
 
@@ -204,8 +207,11 @@ TmEcode ReceivePcapFileLoop(ThreadVars *tv, void *data, void *slot)
 
     if(ptv->is_directory == 0) {
         SCLogInfo("Starting file run for %s", ptv->behavior.file->filename);
+        /* Hold a reference for the duration of file processing, including
+         * post-dispatch flow draining during EngineStop, so deletion decision
+         * is deferred until all pseudo packets have been processed. */
+        SC_ATOMIC_ADD(ptv->behavior.file->ref_cnt, 1);
         status = PcapFileDispatch(ptv->behavior.file);
-        CleanupPcapFileFromThreadVars(ptv, ptv->behavior.file);
     } else {
         SCLogInfo("Starting directory run for %s", ptv->behavior.directory->filename);
         PcapDirectoryDispatch(ptv->behavior.directory);
@@ -215,6 +221,19 @@ TmEcode ReceivePcapFileLoop(ThreadVars *tv, void *data, void *slot)
     SCLogDebug("Pcap file loop complete with status %u", status);
 
     status = PcapFileExit(status, &ptv->shared.last_processed);
+
+    /* Release the hold set before dispatch and trigger deferred cleanup
+     * if requested and this was the final reference. */
+    if (ptv->is_directory == 0) {
+        /* Ensure current pfv global is set for any pseudo packets emitted
+         * during EngineStop/flow drain. */
+        PcapFileSetCurrentPfv(ptv->behavior.file);
+        uint32_t prev = SC_ATOMIC_SUB(ptv->behavior.file->ref_cnt, 1);
+        if (prev == 1 && ptv->behavior.file->cleanup_requested) {
+            CleanupPcapFileFileVars(ptv->behavior.file);
+            ptv->behavior.file = NULL;
+        }
+    }
     SCReturnInt(status);
 }
 
@@ -261,11 +280,7 @@ TmEcode ReceivePcapFileThreadInit(ThreadVars *tv, const void *initdata, void **d
         }
     }
 
-    int should_delete = 0;
-    ptv->shared.should_delete = false;
-    if (SCConfGetBool("pcap-file.delete-when-done", &should_delete) == 1) {
-        ptv->shared.should_delete = should_delete == 1;
-    }
+    ptv->shared.delete_mode = PcapFileParseDeleteMode();
 
     DIR *directory = NULL;
     SCLogDebug("checking file or directory %s", (char*)initdata);
@@ -422,6 +437,11 @@ TmEcode ReceivePcapFileThreadDeinit(ThreadVars *tv, void *data)
     SCEnter();
     if(data != NULL) {
         PcapFileThreadVars *ptv = (PcapFileThreadVars *) data;
+
+        if (!ptv->is_directory && ptv->behavior.file != NULL) {
+            CleanupPcapFileFromThreadVars(ptv, ptv->behavior.file);
+        }
+
         CleanupPcapFileThreadVars(ptv);
     }
     SCReturnInt(TM_ECODE_OK);
diff --git a/src/source-pcap.h b/src/source-pcap.h
index 7fac8e7d9f..489b01f67c 100644
--- a/src/source-pcap.h
+++ b/src/source-pcap.h
@@ -24,6 +24,8 @@
 #ifndef SURICATA_SOURCE_PCAP_H
 #define SURICATA_SOURCE_PCAP_H
 
+typedef struct PcapFileFileVars_ PcapFileFileVars;
+
 void TmModuleReceivePcapRegister (void);
 void TmModuleDecodePcapRegister (void);
 void PcapTranslateIPToDevice(char *pcap_dev, size_t len);
@@ -35,6 +37,7 @@ void PcapTranslateIPToDevice(char *pcap_dev, size_t len);
 typedef struct PcapPacketVars_ {
     uint64_t pcap_cnt;
     uint32_t tenant_id;
+    PcapFileFileVars *pfv;
 } PcapPacketVars;
 
 /** needs to be able to contain Windows adapter id's, so
diff --git a/src/tm-threads.c b/src/tm-threads.c
index 5d3d577b19..647ba83598 100644
--- a/src/tm-threads.c
+++ b/src/tm-threads.c
@@ -35,6 +35,7 @@
 #include "tm-queues.h"
 #include "tm-queuehandlers.h"
 #include "tm-threads.h"
+#include "capture-hooks.h"
 #include "tmqh-packetpool.h"
 #include "threads.h"
 #include "util-affinity.h"
@@ -46,6 +47,7 @@
 #include "util-signal.h"
 #include "queue.h"
 #include "util-validate.h"
+#include "source-pcap-file-helper.h"
 
 #ifdef PROFILE_LOCKING
 thread_local uint64_t mutex_lock_contention;
@@ -1358,6 +1360,7 @@ again:
             if (p != NULL) {
                 p->flags |= PKT_PSEUDO_STREAM_END;
                 PKT_SET_SRC(p, PKT_SRC_SHUTDOWN_FLUSH);
+                CaptureHooksOnPseudoPacketCreated(p);
                 PacketQueue *q = tv->stream_pq;
                 SCMutexLock(&q->mutex_q);
                 PacketEnqueue(q, p);
@@ -1441,6 +1444,7 @@ again:
                 if (p != NULL) {
                     p->flags |= PKT_PSEUDO_STREAM_END;
                     PKT_SET_SRC(p, PKT_SRC_SHUTDOWN_FLUSH);
+                    CaptureHooksOnPseudoPacketCreated(p);
                     PacketQueue *q = tv->stream_pq;
                     SCMutexLock(&q->mutex_q);
                     PacketEnqueue(q, p);
diff --git a/suricata.yaml.in b/suricata.yaml.in
index 3b29513f9d..950856befe 100644
--- a/suricata.yaml.in
+++ b/suricata.yaml.in
@@ -896,7 +896,9 @@ pcap-file:
   # buffer-size: 128 KiB
 
   # tenant-id: none # applies in multi-tenant environment with "direct" selector
-  # delete-when-done: false # applies to file and directory
+  # Applies to file and directory. Options: false (no deletion), true (always delete),
+  #   "non-alerts" (delete only files with no alerts)
+  # delete-when-done: false
 
   # PCAP Directory Processing options
   # recursive: false