diff --git a/readthedocs/config/config.py b/readthedocs/config/config.py
index 68b4d0f62ca..a51ed0d2679 100644
--- a/readthedocs/config/config.py
+++ b/readthedocs/config/config.py
@@ -938,13 +938,9 @@ def validate_python(self):
         ]
 
         with self.catch_validation_error('python.system_packages'):
-            system_packages = self.defaults.get(
-                'use_system_packages',
-                False,
-            )
             system_packages = self.pop_config(
                 'python.system_packages',
-                system_packages,
+                False,
             )
             python['use_system_site_packages'] = validate_bool(system_packages)
 
diff --git a/readthedocs/config/tests/test_config.py b/readthedocs/config/tests/test_config.py
index 4068c3c9ced..9850b9c79f2 100644
--- a/readthedocs/config/tests/test_config.py
+++ b/readthedocs/config/tests/test_config.py
@@ -1604,25 +1604,23 @@ def test_python_system_packages_check_default(self):
         build.validate()
         assert build.python.use_system_site_packages is False
 
-    def test_python_system_packages_respects_default(self):
+    def test_python_system_packages_dont_respects_default(self):
         build = self.get_build_config(
             {},
             {'defaults': {'use_system_packages': True}},
         )
         build.validate()
-        assert build.python.use_system_site_packages is True
+        assert build.python.use_system_site_packages is False
 
     def test_python_system_packages_priority_over_default(self):
         build = self.get_build_config(
             {'python': {'system_packages': False}},
-            {'defaults': {'use_system_packages': True}},
         )
         build.validate()
         assert build.python.use_system_site_packages is False
 
         build = self.get_build_config(
             {'python': {'system_packages': True}},
-            {'defaults': {'use_system_packages': False}},
         )
         build.validate()
         assert build.python.use_system_site_packages is True
diff --git a/readthedocs/rtd_tests/tests/test_config_integration.py b/readthedocs/rtd_tests/tests/test_config_integration.py
index f8928be5526..c927aa6692b 100644
--- a/readthedocs/rtd_tests/tests/test_config_integration.py
+++ b/readthedocs/rtd_tests/tests/test_config_integration.py
@@ -767,6 +767,38 @@ def test_system_packages(self, run, checkout_path, tmpdir):
         assert '--system-site-packages' in args
         assert config.python.use_system_site_packages
 
+    @patch('readthedocs.doc_builder.environments.BuildEnvironment.run')
+    def test_system_packages_project_overrides(self, run, checkout_path, tmpdir):
+
+        # Define `project.use_system_packages` as if it was marked in the Advanced settings.
+        self.version.project.use_system_packages = True
+        self.version.project.save()
+
+        checkout_path.return_value = str(tmpdir)
+        self.create_config_file(
+            tmpdir,
+            {
+                # Do not define `system_packages: True` in the config file.
+                'python': {},
+            },
+        )
+
+        update_docs = self.get_update_docs_task()
+        config = update_docs.config
+
+        python_env = Virtualenv(
+            version=self.version,
+            build_env=update_docs.build_env,
+            config=config,
+        )
+        update_docs.python_env = python_env
+        update_docs.python_env.setup_base()
+
+        args, kwargs = run.call_args
+
+        assert '--system-site-packages' not in args
+        assert not config.python.use_system_site_packages
+
     @pytest.mark.parametrize(
         'value,result',
         [