diff --git a/tools/test_build_system/conftest.py b/tools/test_build_system/conftest.py
index fa9e9cb815..4cf7f5e570 100644
--- a/tools/test_build_system/conftest.py
+++ b/tools/test_build_system/conftest.py
@@ -349,6 +349,24 @@ def pytest_report_header(config: Config) -> str:
         return 'Testing ESP-IDF CMake-based build system v1'
 
 
+@pytest.fixture
+def clean_root_managed_components(tmp_path: Path) -> typing.Generator[None, None, None]:
+    """
+    Temporarily clear root managed components and restore them after the test.
+    """
+    from idf_component_tools.config import root_managed_components_dir
+
+    root_managed = str(root_managed_components_dir())
+    backup = tmp_path / 'root_managed_backup'
+    if os.path.isdir(root_managed):
+        shutil.copytree(root_managed, backup)
+        shutil.rmtree(root_managed)
+    yield
+    shutil.rmtree(root_managed, ignore_errors=True)
+    if backup.is_dir():
+        shutil.copytree(str(backup), root_managed)
+
+
 @pytest.fixture(autouse=True)
 def revert_later(request: FixtureRequest) -> typing.Generator[None, None, None]:
     origin_content_d: dict[str, str] = {}
diff --git a/tools/test_build_system/test_component_manager.py b/tools/test_build_system/test_component_manager.py
index 247468c2fb..c68131a7b1 100644
--- a/tools/test_build_system/test_component_manager.py
+++ b/tools/test_build_system/test_component_manager.py
@@ -1,4 +1,4 @@
-# SPDX-FileCopyrightText: 2022-2025 Espressif Systems (Shanghai) CO LTD
+# SPDX-FileCopyrightText: 2022-2026 Espressif Systems (Shanghai) CO LTD
 # SPDX-License-Identifier: Apache-2.0
 import json
 import os.path
@@ -208,6 +208,10 @@ class TestOptionalDependencyWithKconfig:
 @pytest.mark.buildv2_skip('Root components (idf_extra_components.yml) not yet supported in cmakev2')
 @pytest.mark.revert_later(['tools/idf_extra_components.yml'])
 class TestIdfRootDependency:
+    @pytest.fixture(autouse=True)
+    def _clean_root_managed(self, clean_root_managed_components: None) -> None:
+        pass
+
     def test_basic_build(self, idf_py: IdfPyFunc, test_app_copy: Path) -> None:
         with open(os.path.join(EXT_IDF_PATH, 'tools', 'idf_extra_components.yml'), 'w') as fw:
             fw.write(
diff --git a/tools/test_build_system/test_components.py b/tools/test_build_system/test_components.py
index c5b226a4b3..5f9ec17b5e 100644
--- a/tools/test_build_system/test_components.py
+++ b/tools/test_build_system/test_components.py
@@ -246,7 +246,9 @@ def test_extra_components_overrides_managed_components(idf_py: IdfPyFunc, test_a
 
 
 @pytest.mark.with_idf_components(['cmp'])
-def test_managed_components_overrides_idf_components(idf_py: IdfPyFunc, test_app_copy: Path) -> None:
+def test_managed_components_overrides_idf_components(
+    idf_py: IdfPyFunc, test_app_copy: Path, clean_root_managed_components: None
+) -> None:
     logging.info('Managed components override components defined in IDF_PATH/components')
     # created idf component 'cmp' in marker
     idf_path = Path(os.environ['IDF_PATH'])