diff --git a/.gitlab/ci/host-test.yml b/.gitlab/ci/host-test.yml
index 6d32d7c82e4..24c995585b6 100644
--- a/.gitlab/ci/host-test.yml
+++ b/.gitlab/ci/host-test.yml
@@ -483,6 +483,7 @@ pytest_buildv2_system:
       --junitxml ${CI_PROJECT_DIR}/XUNIT_RESULT.xml
       --ignore-result-files ${KNOWN_FAILURE_CASES_FILE_NAME}
       --
+      buildv2
       test_non_default_target.py
       test_component_manager.py
       test_build.py
diff --git a/.gitlab/ci/test-win.yml b/.gitlab/ci/test-win.yml
index c617358959f..bb4ab49a5de 100644
--- a/.gitlab/ci/test-win.yml
+++ b/.gitlab/ci/test-win.yml
@@ -171,6 +171,7 @@ pytest_buildv2_system_win:
       --junitxml=${CI_PROJECT_DIR}\XUNIT_RESULT.xml
       --ignore-result-files ${KNOWN_FAILURE_CASES_FILE_NAME}
       --
+      buildv2
       test_non_default_target.py
       test_component_manager.py
       test_build.py
diff --git a/tools/test_build_system/conftest.py b/tools/test_build_system/conftest.py
index 69ca91e6b5e..d8d85ce0a0e 100644
--- a/tools/test_build_system/conftest.py
+++ b/tools/test_build_system/conftest.py
@@ -241,13 +241,18 @@ def idf_py(default_idf_env: EnvDict) -> IdfPyFunc:
 
 
 def pytest_collection_modifyitems(session: Session, config: Config, items: list[Item]) -> None:
-    if not config.getoption('--buildv2', False):
-        return
+    buildv2_dir = Path(__file__).parent / 'buildv2'
+    is_buildv2 = config.getoption('--buildv2', False)
+
     for item in items:
-        marker = item.get_closest_marker('buildv2_skip')
-        if marker:
-            reason = marker.args[0] if marker.args else 'Skipped as this test is specific to build system v1.'
-            item.add_marker(pytest.mark.skip(reason=reason))
+        if is_buildv2:
+            marker = item.get_closest_marker('buildv2_skip')
+            if marker:
+                reason = marker.args[0] if marker.args else 'Skipped as this test is specific to build system v1.'
+                item.add_marker(pytest.mark.skip(reason=reason))
+        else:
+            if buildv2_dir in item.path.parents or item.path == buildv2_dir:
+                item.add_marker(pytest.mark.skip(reason='Skipped as build system v2 tests are disabled.'))
 
 
 def pytest_report_header(config: Config) -> str: