diff --git a/esphome/writer.py b/esphome/writer.py
index cf04e4f8d2a..72c2c355dcc 100644
--- a/esphome/writer.py
+++ b/esphome/writer.py
@@ -490,6 +490,14 @@ def clean_build(clear_pio_cache: bool = True):
     if dependencies_lock.is_file():
         _LOGGER.info("Deleting %s", dependencies_lock)
         dependencies_lock.unlink()
+    # Native ESP-IDF toolchain artifacts: the IDF CMake/ninja build dir
+    # and the Component Manager's fetched managed components live under
+    # the project's build path, not under .pioenvs / .piolibdeps.
+    for name in ("build", "managed_components"):
+        idf_path = CORE.relative_build_path(name)
+        if idf_path.is_dir():
+            _LOGGER.info("Deleting %s", idf_path)
+            rmtree(idf_path)
 
     if not clear_pio_cache:
         return
diff --git a/tests/unit_tests/test_writer.py b/tests/unit_tests/test_writer.py
index e76769e6a83..91b4bd8e87b 100644
--- a/tests/unit_tests/test_writer.py
+++ b/tests/unit_tests/test_writer.py
@@ -443,6 +443,14 @@ def test_clean_build(
     dependencies_lock = tmp_path / "dependencies.lock"
     dependencies_lock.write_text("lock file")
 
+    # Native ESP-IDF toolchain artifacts.
+    idf_build_dir = tmp_path / "build"
+    idf_build_dir.mkdir()
+    (idf_build_dir / "CMakeCache.txt").write_text("cache")
+    managed_components_dir = tmp_path / "managed_components"
+    managed_components_dir.mkdir()
+    (managed_components_dir / "espressif__arduino-esp32").mkdir()
+
     # Create PlatformIO cache directory
     platformio_cache_dir = tmp_path / ".platformio" / ".cache"
     platformio_cache_dir.mkdir(parents=True)
@@ -454,12 +462,14 @@ def test_clean_build(
     # Setup mocks
     mock_core.relative_pioenvs_path.return_value = pioenvs_dir
     mock_core.relative_piolibdeps_path.return_value = piolibdeps_dir
-    mock_core.relative_build_path.return_value = dependencies_lock
+    mock_core.relative_build_path.side_effect = lambda name: tmp_path / name
 
     # Verify all exist before
     assert pioenvs_dir.exists()
     assert piolibdeps_dir.exists()
     assert dependencies_lock.exists()
+    assert idf_build_dir.exists()
+    assert managed_components_dir.exists()
     assert platformio_cache_dir.exists()
 
     # Mock PlatformIO's ProjectConfig cache_dir
@@ -482,6 +492,8 @@ def test_clean_build(
     assert not pioenvs_dir.exists()
     assert not piolibdeps_dir.exists()
     assert not dependencies_lock.exists()
+    assert not idf_build_dir.exists()
+    assert not managed_components_dir.exists()
     assert not platformio_cache_dir.exists()
 
     # Verify logging
@@ -489,6 +501,8 @@ def test_clean_build(
     assert ".pioenvs" in caplog.text
     assert ".piolibdeps" in caplog.text
     assert "dependencies.lock" in caplog.text
+    assert str(idf_build_dir) in caplog.text
+    assert str(managed_components_dir) in caplog.text
     assert "PlatformIO cache" in caplog.text
 
 
@@ -510,7 +524,7 @@ def test_clean_build_partial_exists(
     # Setup mocks
     mock_core.relative_pioenvs_path.return_value = pioenvs_dir
     mock_core.relative_piolibdeps_path.return_value = piolibdeps_dir
-    mock_core.relative_build_path.return_value = dependencies_lock
+    mock_core.relative_build_path.side_effect = lambda name: tmp_path / name
 
     # Verify only pioenvs exists
     assert pioenvs_dir.exists()
@@ -547,7 +561,7 @@ def test_clean_build_nothing_exists(
     # Setup mocks
     mock_core.relative_pioenvs_path.return_value = pioenvs_dir
     mock_core.relative_piolibdeps_path.return_value = piolibdeps_dir
-    mock_core.relative_build_path.return_value = dependencies_lock
+    mock_core.relative_build_path.side_effect = lambda name: tmp_path / name
 
     # Verify nothing exists
     assert not pioenvs_dir.exists()
@@ -583,7 +597,7 @@ def test_clean_build_platformio_not_available(
     # Setup mocks
     mock_core.relative_pioenvs_path.return_value = pioenvs_dir
     mock_core.relative_piolibdeps_path.return_value = piolibdeps_dir
-    mock_core.relative_build_path.return_value = dependencies_lock
+    mock_core.relative_build_path.side_effect = lambda name: tmp_path / name
 
     # Verify all exist before
     assert pioenvs_dir.exists()
@@ -621,7 +635,7 @@ def test_clean_build_empty_cache_dir(
     # Setup mocks
     mock_core.relative_pioenvs_path.return_value = pioenvs_dir
     mock_core.relative_piolibdeps_path.return_value = tmp_path / ".piolibdeps"
-    mock_core.relative_build_path.return_value = tmp_path / "dependencies.lock"
+    mock_core.relative_build_path.side_effect = lambda name: tmp_path / name
 
     # Verify pioenvs exists before
     assert pioenvs_dir.exists()
@@ -1349,7 +1363,7 @@ def test_clean_build_handles_readonly_files(
     # Setup mocks
     mock_core.relative_pioenvs_path.return_value = pioenvs_dir
     mock_core.relative_piolibdeps_path.return_value = tmp_path / ".piolibdeps"
-    mock_core.relative_build_path.return_value = tmp_path / "dependencies.lock"
+    mock_core.relative_build_path.side_effect = lambda name: tmp_path / name
 
     # Verify file is read-only
     assert not os.access(readonly_file, os.W_OK)
@@ -1413,7 +1427,7 @@ def test_clean_build_reraises_for_other_errors(
     # Setup mocks
     mock_core.relative_pioenvs_path.return_value = pioenvs_dir
     mock_core.relative_piolibdeps_path.return_value = tmp_path / ".piolibdeps"
-    mock_core.relative_build_path.return_value = tmp_path / "dependencies.lock"
+    mock_core.relative_build_path.side_effect = lambda name: tmp_path / name
 
     try:
         # Mock os.access in writer module to return True (writable)