diff --git a/changelog/13484.bugfix.rst b/changelog/13484.bugfix.rst
new file mode 100644
index 00000000000..4572794cea2
--- /dev/null
+++ b/changelog/13484.bugfix.rst
@@ -0,0 +1 @@
+Fixed ``-W`` option values being duplicated in ``Config.known_args_namespace`` when using ``action="append"`` options.
diff --git a/src/_pytest/config/__init__.py b/src/_pytest/config/__init__.py
index 86786c2b04a..5c489b1f539 100644
--- a/src/_pytest/config/__init__.py
+++ b/src/_pytest/config/__init__.py
@@ -1533,7 +1533,9 @@ 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.copy(self.option)
+        )
 
         self._validate_plugins()
         self._warn_about_skipped_plugins()
diff --git a/testing/test_warnings.py b/testing/test_warnings.py
index d4a5038d5d2..e2363bd884a 100644
--- a/testing/test_warnings.py
+++ b/testing/test_warnings.py
@@ -1038,3 +1038,12 @@ def test_one():
         result = pytester.runpytest()
         result.assert_outcomes(passed=1, warnings=1)
         assert result.ret == ExitCode.OK
+
+
+def test_pythonwarnings_not_duplicated(pytester: Pytester) -> None:
+    """Regression test for #13484: -W values should not be duplicated in
+    known_args_namespace due to the arg parser being called multiple times."""
+    config = pytester.parseconfig("-W", "error")
+    warnings_list = config.known_args_namespace.pythonwarnings
+    assert warnings_list is not None
+    assert warnings_list == ["error"]