diff --git a/certbot/plugins/standalone.py b/certbot/plugins/standalone.py
index f3cd4b49d..0195b2726 100644
--- a/certbot/plugins/standalone.py
+++ b/certbot/plugins/standalone.py
@@ -13,6 +13,7 @@ import zope.interface
 from acme import challenges
 from acme import standalone as acme_standalone
 
+from certbot import cli
 from certbot import errors
 from certbot import interfaces
 
@@ -120,10 +121,11 @@ def supported_challenges_validator(data):
     It should be passed as `type` argument to `add_argument`.
 
     """
-    sys.stderr.write(
-        "WARNING: The standalone specific "
-        "supported challenges flag is deprecated\n")
-    sys.stderr.write("Please use the --preferred-challenges flag instead.\n")
+    if cli.set_by_cli("standalone_supported_challenges"):
+        sys.stderr.write(
+            "WARNING: The standalone specific "
+            "supported challenges flag is deprecated.\n"
+            "Please use the --preferred-challenges flag instead.\n")
     challs = data.split(",")
 
     # tls-sni-01 was dvsni during private beta
diff --git a/certbot/plugins/standalone_test.py b/certbot/plugins/standalone_test.py
index eb6631732..1dfa3950a 100644
--- a/certbot/plugins/standalone_test.py
+++ b/certbot/plugins/standalone_test.py
@@ -67,10 +67,25 @@ class ServerManagerTest(unittest.TestCase):
 class SupportedChallengesValidatorTest(unittest.TestCase):
     """Tests for plugins.standalone.supported_challenges_validator."""
 
+    def setUp(self):
+        self.set_by_cli_patch = mock.patch(
+            "certbot.plugins.standalone.cli.set_by_cli")
+        self.stderr_patch = mock.patch("certbot.plugins.standalone.sys.stderr")
+
+        self.set_by_cli_patch.start().return_value = True
+        self.stderr = self.stderr_patch.start()
+
+    def tearDown(self):
+        self.set_by_cli_patch.stop()
+        self.stderr_patch.stop()
+
     def _call(self, data):
         from certbot.plugins.standalone import (
             supported_challenges_validator)
-        return supported_challenges_validator(data)
+        return_value = supported_challenges_validator(data)
+        self.assertTrue(self.stderr.write.called)  # pylint: disable=no-member
+        self.stderr.write.reset_mock()  # pylint: disable=no-member
+        return return_value
 
     def test_correct(self):
         self.assertEqual("tls-sni-01", self._call("tls-sni-01"))