diff --git a/esphome/__main__.py b/esphome/__main__.py
index b0c081a34f..f8fb678cb2 100644
--- a/esphome/__main__.py
+++ b/esphome/__main__.py
@@ -1319,7 +1319,7 @@ def parse_args(argv):
         "clean-all", help="Clean all build and platform files."
     )
     parser_clean_all.add_argument(
-        "configuration", help="Your YAML configuration directory.", nargs="*"
+        "configuration", help="Your YAML file or configuration directory.", nargs="*"
     )
 
     parser_dashboard = subparsers.add_parser(
diff --git a/esphome/writer.py b/esphome/writer.py
index 8eee445cf1..1e49a2c961 100644
--- a/esphome/writer.py
+++ b/esphome/writer.py
@@ -340,7 +340,13 @@ def clean_build():
 def clean_all(configuration: list[str]):
     import shutil
 
-    data_dirs = [Path(dir) / ".esphome" for dir in configuration]
+    data_dirs = []
+    for config in configuration:
+        item = Path(config)
+        if item.is_file() and item.suffix in (".yaml", ".yml"):
+            data_dirs.append(item.parent / ".esphome")
+        else:
+            data_dirs.append(item / ".esphome")
     if is_ha_addon():
         data_dirs.append(Path("/data"))
     if "ESPHOME_DATA_DIR" in os.environ:
diff --git a/tests/unit_tests/test_writer.py b/tests/unit_tests/test_writer.py
index a4490fbbc0..a2a358f4d3 100644
--- a/tests/unit_tests/test_writer.py
+++ b/tests/unit_tests/test_writer.py
@@ -737,6 +737,37 @@ def test_write_cpp_with_duplicate_markers(
         write_cpp("// New code")
 
 
+@patch("esphome.writer.CORE")
+def test_clean_all_with_yaml_file(
+    mock_core: MagicMock,
+    tmp_path: Path,
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """Test clean_all with a .yaml file uses parent directory."""
+    # Create config directory with yaml file
+    config_dir = tmp_path / "config"
+    config_dir.mkdir()
+    yaml_file = config_dir / "test.yaml"
+    yaml_file.write_text("esphome:\n  name: test\n")
+
+    build_dir = config_dir / ".esphome"
+    build_dir.mkdir()
+    (build_dir / "dummy.txt").write_text("x")
+
+    from esphome.writer import clean_all
+
+    with caplog.at_level("INFO"):
+        clean_all([str(yaml_file)])
+
+    # Verify .esphome directory still exists but contents cleaned
+    assert build_dir.exists()
+    assert not (build_dir / "dummy.txt").exists()
+
+    # Verify logging mentions the build dir
+    assert "Cleaning" in caplog.text
+    assert str(build_dir) in caplog.text
+
+
 @patch("esphome.writer.CORE")
 def test_clean_all(
     mock_core: MagicMock,