diff --git a/src/borg/repository.py b/src/borg/repository.py
index f02224e86..d538a37a5 100644
--- a/src/borg/repository.py
+++ b/src/borg/repository.py
@@ -1225,11 +1225,11 @@ class Repository:
         except KeyError:
             pass
         else:
-            # note: doing a delete first will do some bookkeeping.
-            # we do not want to update the shadow_index here, because
-            # we know already that we will PUT to this id, so it will
-            # be in the repo index (and we won't need it in the shadow_index).
-            self._delete(id, segment, offset, update_shadow_index=False)
+            # this put call supersedes a previous put to same id.
+            # it is essential to do a delete first to get correct quota bookkeeping
+            # and also a correctly updated shadow_index, so that the compaction code
+            # does not wrongly resurrect an old PUT by dropping a DEL that is still needed.
+            self._delete(id, segment, offset)
         segment, offset = self.io.write_put(id, data)
         self.storage_quota_use += len(data) + self.io.put_header_fmt.size
         self.segments.setdefault(segment, 0)
@@ -1252,16 +1252,15 @@ class Repository:
             segment, offset = self.index.pop(id)
         except KeyError:
             raise self.ObjectNotFound(id, self.path) from None
-        # if we get here, there is an object with this id in the repo,
-        # we write a DEL here that shadows the respective PUT.
-        # after the delete, the object is not in the repo index any more,
-        # for the compaction code, we need to update the shadow_index in this case.
-        self._delete(id, segment, offset, update_shadow_index=True)
+        self._delete(id, segment, offset)
 
-    def _delete(self, id, segment, offset, *, update_shadow_index):
+    def _delete(self, id, segment, offset):
         # common code used by put and delete
-        if update_shadow_index:
-            self.shadow_index.setdefault(id, []).append(segment)
+        # because we'll write a DEL tag to the repository, we must update the shadow index.
+        # this is always true, no matter whether we are called from put() or delete().
+        # the compaction code needs this to not drop DEL tags if they are still required
+        # to keep a PUT in an earlier segment in the "effectively deleted" state.
+        self.shadow_index.setdefault(id, []).append(segment)
         self.segments[segment] -= 1
         size = self.io.read(segment, offset, id, read_data=False)
         self.compact[segment] += size
diff --git a/src/borg/testsuite/repository.py b/src/borg/testsuite/repository.py
index 39017d72a..b537ccc81 100644
--- a/src/borg/testsuite/repository.py
+++ b/src/borg/testsuite/repository.py
@@ -345,7 +345,8 @@ class RepositoryCommitTestCase(RepositoryTestCaseBase):
         # we have no put or del any more for H(1), so we lost knowledge about H(1).
         assert H(1) not in self.repository.shadow_index
 
-    def test_shadowed_entries_are_preserved(self):
+    def test_shadowed_entries_are_preserved1(self):
+        # this tests the shadowing-by-del behaviour
         get_latest_segment = self.repository.io.get_latest_segment
         self.repository.put(H(1), b'1')
         # This is the segment with our original PUT of interest
@@ -379,6 +380,54 @@ class RepositoryCommitTestCase(RepositoryTestCaseBase):
         # Must not reappear
         assert H(1) not in self.repository
 
+    def test_shadowed_entries_are_preserved2(self):
+        # this tests the shadowing-by-double-put behaviour, see issue #5661
+        # assume this repo state:
+        # seg1: PUT H1
+        # seg2: COMMIT
+        # seg3: DEL H1, PUT H1, DEL H1, PUT H2
+        # seg4: COMMIT
+        # Note how due to the final DEL H1 in seg3, H1 is effectively deleted.
+        #
+        # compaction of only seg3:
+        # PUT H1 gets dropped because it is not needed any more.
+        # DEL H1 must be kept, because there is still a PUT H1 in seg1 which must not
+        # "reappear" in the index if the index gets rebuilt.
+        get_latest_segment = self.repository.io.get_latest_segment
+        self.repository.put(H(1), b'1')
+        # This is the segment with our original PUT of interest
+        put_segment = get_latest_segment()
+        self.repository.commit(compact=False)
+
+        # We now put H(1) again (which implicitly does DEL(H(1)) followed by PUT(H(1), ...)),
+        # delete H(1) afterwards, and force this segment to not be compacted, which can happen
+        # if it's not sparse enough (symbolized by H(2) here).
+        self.repository.put(H(1), b'1')
+        self.repository.delete(H(1))
+        self.repository.put(H(2), b'1')
+        delete_segment = get_latest_segment()
+
+        # We pretend these are mostly dense (not sparse) and won't be compacted
+        del self.repository.compact[put_segment]
+        del self.repository.compact[delete_segment]
+
+        self.repository.commit(compact=True)
+
+        # Now we perform an unrelated operation on the segment containing the DELETE,
+        # causing it to be compacted.
+        self.repository.delete(H(2))
+        self.repository.commit(compact=True)
+
+        assert self.repository.io.segment_exists(put_segment)
+        assert not self.repository.io.segment_exists(delete_segment)
+
+        # Basic case, since the index survived this must be ok
+        assert H(1) not in self.repository
+        # Nuke index, force replay
+        os.unlink(os.path.join(self.repository.path, 'index.%d' % get_latest_segment()))
+        # Must not reappear
+        assert H(1) not in self.repository
+
     def test_shadow_index_rollback(self):
         self.repository.put(H(1), b'1')
         self.repository.delete(H(1))