diff --git a/esphome/writer.py b/esphome/writer.py
index b5cfd9b667..8eee445cf1 100644
--- a/esphome/writer.py
+++ b/esphome/writer.py
@@ -15,6 +15,8 @@ from esphome.const import (
 from esphome.core import CORE, EsphomeError
 from esphome.helpers import (
     copy_file_if_changed,
+    get_str_env,
+    is_ha_addon,
     read_file,
     walk_files,
     write_file_if_changed,
@@ -338,16 +340,21 @@ def clean_build():
 def clean_all(configuration: list[str]):
     import shutil
 
-    # Clean entire build dir
-    for dir in configuration:
-        build_dir = Path(dir) / ".esphome"
-        if build_dir.is_dir():
-            _LOGGER.info("Cleaning %s", build_dir)
-            # Don't remove storage as it will cause the dashboard to regenerate all configs
-            for item in build_dir.iterdir():
-                if item.is_file():
+    data_dirs = [Path(dir) / ".esphome" for dir in configuration]
+    if is_ha_addon():
+        data_dirs.append(Path("/data"))
+    if "ESPHOME_DATA_DIR" in os.environ:
+        data_dirs.append(Path(get_str_env("ESPHOME_DATA_DIR", None)))
+
+    # Clean build dir
+    for dir in data_dirs:
+        if dir.is_dir():
+            _LOGGER.info("Cleaning %s", dir)
+            # Don't remove storage or .json files which are needed by the dashboard
+            for item in dir.iterdir():
+                if item.is_file() and not item.name.endswith(".json"):
                     item.unlink()
-                elif item.name != "storage" and item.is_dir():
+                elif item.is_dir() and item.name != "storage":
                     shutil.rmtree(item)
 
     # Clean PlatformIO project files
diff --git a/tests/unit_tests/test_writer.py b/tests/unit_tests/test_writer.py
index bffd2b3881..a4490fbbc0 100644
--- a/tests/unit_tests/test_writer.py
+++ b/tests/unit_tests/test_writer.py
@@ -985,3 +985,49 @@ def test_clean_all_removes_non_storage_directories(
     # Verify logging mentions cleaning
     assert "Cleaning" in caplog.text
     assert str(build_dir) in caplog.text
+
+
+@patch("esphome.writer.CORE")
+def test_clean_all_preserves_json_files(
+    mock_core: MagicMock,
+    tmp_path: Path,
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """Test clean_all preserves .json files."""
+    # Create build directory with various files
+    config_dir = tmp_path / "config"
+    config_dir.mkdir()
+
+    build_dir = config_dir / ".esphome"
+    build_dir.mkdir()
+
+    # Create .json files (should be preserved)
+    (build_dir / "config.json").write_text('{"config": "data"}')
+    (build_dir / "metadata.json").write_text('{"metadata": "info"}')
+
+    # Create non-.json files (should be removed)
+    (build_dir / "dummy.txt").write_text("x")
+    (build_dir / "other.log").write_text("log content")
+
+    # Call clean_all
+    from esphome.writer import clean_all
+
+    with caplog.at_level("INFO"):
+        clean_all([str(config_dir)])
+
+    # Verify .esphome directory still exists
+    assert build_dir.exists()
+
+    # Verify .json files are preserved
+    assert (build_dir / "config.json").exists()
+    assert (build_dir / "config.json").read_text() == '{"config": "data"}'
+    assert (build_dir / "metadata.json").exists()
+    assert (build_dir / "metadata.json").read_text() == '{"metadata": "info"}'
+
+    # Verify non-.json files were removed
+    assert not (build_dir / "dummy.txt").exists()
+    assert not (build_dir / "other.log").exists()
+
+    # Verify logging mentions cleaning
+    assert "Cleaning" in caplog.text
+    assert str(build_dir) in caplog.text