diff --git a/changelog/4013.feature.rst b/changelog/4013.feature.rst
new file mode 100644
index 000000000..84c3ab79d
--- /dev/null
+++ b/changelog/4013.feature.rst
@@ -0,0 +1,2 @@
+Deprecation warnings are now shown even if you customize the warnings filters yourself. In the previous version
+any customization would override pytest's filters and deprecation warnings would fall back to being hidden by default.
diff --git a/doc/en/warnings.rst b/doc/en/warnings.rst
index 1f0c3bf97..07aec9855 100644
--- a/doc/en/warnings.rst
+++ b/doc/en/warnings.rst
@@ -101,22 +101,28 @@ DeprecationWarning and PendingDeprecationWarning
 ------------------------------------------------
 
 .. versionadded:: 3.8
+.. versionchanged:: 3.9
 
-By default pytest will display ``DeprecationWarning`` and ``PendingDeprecationWarning`` if no other warning filters
-are configured.
+By default pytest will display ``DeprecationWarning`` and ``PendingDeprecationWarning``.
 
-To disable showing ``DeprecationWarning`` and ``PendingDeprecationWarning`` warnings, you might define any warnings
-filter either in the command-line or in the ini file, or you can use:
+Sometimes it is useful to hide some specific deprecation warnings that happen in code that you have no control over
+(such as third-party libraries), in which case you might use the standard warning filters options (ini or marks).
+For example:
 
 .. code-block:: ini
 
     [pytest]
     filterwarnings =
-        ignore::DeprecationWarning
-        ignore::PendingDeprecationWarning
+        ignore:.*U.*mode is deprecated:DeprecationWarning
+
 
 .. note::
-    This makes pytest more compliant with `PEP-0506 <https://www.python.org/dev/peps/pep-0565/#recommended-filter-settings-for-test-runners>`_ which suggests that those warnings should
+    If warnings are configured at the interpreter level, using
+    the `PYTHONWARNINGS <https://docs.python.org/3/using/cmdline.html#envvar-PYTHONWARNINGS>`_ environment variable or the
+    ``-W`` command-line option, pytest will not configure any filters by default.
+
+.. note::
+    This feature makes pytest more compliant with `PEP-0506 <https://www.python.org/dev/peps/pep-0565/#recommended-filter-settings-for-test-runners>`_ which suggests that those warnings should
     be shown by default by test runners, but pytest doesn't follow ``PEP-0506`` completely because resetting all
     warning filters like suggested in the PEP will break existing test suites that configure warning filters themselves
     by calling ``warnings.simplefilter`` (see issue `#2430 <https://github.com/pytest-dev/pytest/issues/2430>`_
diff --git a/src/_pytest/warnings.py b/src/_pytest/warnings.py
index fb303a20f..5574eee8e 100644
--- a/src/_pytest/warnings.py
+++ b/src/_pytest/warnings.py
@@ -70,7 +70,11 @@ def catch_warnings_for_item(config, ihook, when, item):
     cmdline_filters = config.getoption("pythonwarnings") or []
     inifilters = config.getini("filterwarnings")
     with warnings.catch_warnings(record=True) as log:
-        filters_configured = bool(cmdline_filters or inifilters or sys.warnoptions)
+
+        if not sys.warnoptions:
+            # if user is not explicitly configuring warning filters, show deprecation warnings by default (#2908)
+            warnings.filterwarnings("always", category=DeprecationWarning)
+            warnings.filterwarnings("always", category=PendingDeprecationWarning)
 
         # filters should have this precedence: mark, cmdline options, ini
         # filters should be applied in the inverse order of precedence
@@ -84,12 +88,6 @@ def catch_warnings_for_item(config, ihook, when, item):
             for mark in item.iter_markers(name="filterwarnings"):
                 for arg in mark.args:
                     _setoption(warnings, arg)
-                    filters_configured = True
-
-        if not filters_configured:
-            # if user is not explicitly configuring warning filters, show deprecation warnings by default (#2908)
-            warnings.filterwarnings("always", category=DeprecationWarning)
-            warnings.filterwarnings("always", category=PendingDeprecationWarning)
 
         yield
 
diff --git a/testing/test_warnings.py b/testing/test_warnings.py
index 975605b5e..7825f2167 100644
--- a/testing/test_warnings.py
+++ b/testing/test_warnings.py
@@ -495,8 +495,18 @@ class TestDeprecationWarningsByDefault:
             )
         )
 
-    def test_shown_by_default(self, testdir):
+    @pytest.mark.parametrize("customize_filters", [True, False])
+    def test_shown_by_default(self, testdir, customize_filters):
+        """Show deprecation warnings by default, even if user has customized the warnings filters (#4013)."""
         self.create_file(testdir)
+        if customize_filters:
+            testdir.makeini(
+                """
+                [pytest]
+                filterwarnings =
+                    once::UserWarning
+            """
+            )
         result = testdir.runpytest_subprocess()
         result.stdout.fnmatch_lines(
             [
@@ -512,7 +522,9 @@ class TestDeprecationWarningsByDefault:
         testdir.makeini(
             """
             [pytest]
-            filterwarnings = once::UserWarning
+            filterwarnings =
+                ignore::DeprecationWarning
+                ignore::PendingDeprecationWarning
         """
         )
         result = testdir.runpytest_subprocess()
@@ -523,7 +535,8 @@ class TestDeprecationWarningsByDefault:
         be displayed normally.
         """
         self.create_file(
-            testdir, mark='@pytest.mark.filterwarnings("once::UserWarning")'
+            testdir,
+            mark='@pytest.mark.filterwarnings("ignore::PendingDeprecationWarning")',
         )
         result = testdir.runpytest_subprocess()
         result.stdout.fnmatch_lines(
@@ -536,7 +549,12 @@ class TestDeprecationWarningsByDefault:
 
     def test_hidden_by_cmdline(self, testdir):
         self.create_file(testdir)
-        result = testdir.runpytest_subprocess("-W", "once::UserWarning")
+        result = testdir.runpytest_subprocess(
+            "-W",
+            "ignore::DeprecationWarning",
+            "-W",
+            "ignore::PendingDeprecationWarning",
+        )
         assert WARNINGS_SUMMARY_HEADER not in result.stdout.str()
 
     def test_hidden_by_system(self, testdir, monkeypatch):