diff --git a/changelog/13484.bugfix.rst b/changelog/13484.bugfix.rst
new file mode 100644
index 00000000000..7a37410bce9
--- /dev/null
+++ b/changelog/13484.bugfix.rst
@@ -0,0 +1 @@
+Fixed ``known_args_namespace`` containing duplicate values for append-action arguments like ``-W`` due to re-parsing into the same namespace.
diff --git a/src/_pytest/config/__init__.py b/src/_pytest/config/__init__.py
index 21dc35219d8..0c7c5e1a58e 100644
--- a/src/_pytest/config/__init__.py
+++ b/src/_pytest/config/__init__.py
@@ -1358,7 +1358,7 @@ def _validate_args(self, args: list[str], via: str) -> list[str]:
         self._parser.extra_info["config source"] = via
         try:
             self._parser.parse_known_and_unknown_args(
-                args, namespace=copy.copy(self.option)
+                args, namespace=copy.deepcopy(self.option)
             )
         finally:
             self._parser.extra_info.pop("config source", None)
@@ -1500,7 +1500,7 @@ def parse(self, args: list[str], addopts: bool = True) -> None:
                     + args
                 )
 
-        ns = self._parser.parse_known_args(args, namespace=copy.copy(self.option))
+        ns = self._parser.parse_known_args(args, namespace=copy.deepcopy(self.option))
         rootpath, inipath, inicfg, ignored_config_files = determine_setup(
             inifile=ns.inifilename,
             override_ini=ns.override_ini,
@@ -1533,7 +1533,7 @@ def parse(self, args: list[str], addopts: bool = True) -> None:
             )
 
         self.known_args_namespace = self._parser.parse_known_args(
-            args, namespace=copy.copy(self.option)
+            args, namespace=copy.deepcopy(self.option)
         )
         self._checkversion()
         self._consider_importhook()
@@ -1550,7 +1550,9 @@ def parse(self, args: list[str], addopts: bool = True) -> None:
         # are going to be loaded.
         self.pluginmanager.consider_env()
 
-        self._parser.parse_known_args(args, namespace=self.known_args_namespace)
+        self.known_args_namespace = self._parser.parse_known_args(
+            args, namespace=copy.deepcopy(self.option)
+        )
 
         self._validate_plugins()
         self._warn_about_skipped_plugins()
diff --git a/testing/test_config.py b/testing/test_config.py
index de11e3fa13a..fbd3b9ece5a 100644
--- a/testing/test_config.py
+++ b/testing/test_config.py
@@ -2327,6 +2327,12 @@ def test_addopts_from_ini_not_concatenated(self, pytester: Pytester) -> None:
         )
         assert result.ret == _pytest.config.ExitCode.USAGE_ERROR
 
+    def test_append_args_not_duplicated(self, _config_for_test, _sys_snapshot) -> None:
+        """Append-action args should not be duplicated after multiple parses (#13484)."""
+        config = _config_for_test
+        config.parse(["-Werror"], addopts=True)
+        assert config.known_args_namespace.pythonwarnings == ["error"]
+
     def test_override_ini_does_not_contain_paths(
         self, _config_for_test, _sys_snapshot
     ) -> None: