diff --git a/backend/packages/harness/deerflow/skills/storage/__init__.py b/backend/packages/harness/deerflow/skills/storage/__init__.py
index 7f669e63bb..6d7da6730e 100644
--- a/backend/packages/harness/deerflow/skills/storage/__init__.py
+++ b/backend/packages/harness/deerflow/skills/storage/__init__.py
@@ -128,6 +128,9 @@ def get_or_new_user_skill_storage(user_id: str, **kwargs) -> SkillStorage:
     if app_config is None:
         app_config = get_app_config()
     kwargs["app_config"] = app_config
+    # User-scoped storage must mount skills at the same configured root as
+    # public storage; an explicit caller override still wins.
+    kwargs.setdefault("container_path", app_config.skills.container_path)
 
     # Always acquire lock so move_to_end is safe — makes this a true LRU
     # cache instead of FIFO. The overhead is negligible since dict ops are
@@ -161,6 +164,14 @@ def user_should_see_legacy_skills(user_id: str, **kwargs) -> bool:
     if kwargs:
         from deerflow.config.paths import make_safe_user_id
 
+        # One-off constructions mount at the configured root too, same as the
+        # factory path; an explicit caller override still wins.
+        app_config = kwargs.get("app_config")
+        if app_config is None:
+            from deerflow.config import get_app_config
+
+            app_config = get_app_config()
+        kwargs.setdefault("container_path", app_config.skills.container_path)
         storage = UserScopedSkillStorage(make_safe_user_id(user_id), **kwargs)
     else:
         storage = get_or_new_user_skill_storage(user_id)
diff --git a/backend/tests/test_user_scoped_skill_storage.py b/backend/tests/test_user_scoped_skill_storage.py
index 37cff7eb4e..93a4215eec 100644
--- a/backend/tests/test_user_scoped_skill_storage.py
+++ b/backend/tests/test_user_scoped_skill_storage.py
@@ -13,7 +13,7 @@ import pytest
 from deerflow.config.paths import Paths
 from deerflow.skills.installer import SkillSecurityScanError
 from deerflow.skills.security_scanner import ScanResult
-from deerflow.skills.storage import reset_skill_storage, reset_user_skill_storage
+from deerflow.skills.storage import get_or_new_user_skill_storage, reset_skill_storage, reset_user_skill_storage, user_should_see_legacy_skills
 from deerflow.skills.storage.local_skill_storage import LocalSkillStorage
 from deerflow.skills.storage.user_scoped_skill_storage import UserScopedSkillStorage
 from deerflow.skills.types import SkillCategory
@@ -103,6 +103,33 @@ class TestPathRedirection:
         assert user_storage.user_id == "test-user"
 
 
+class TestFactoryContainerPath:
+    """get_or_new_user_skill_storage must mount skills at the configured root,
+    same as the public-storage factory."""
+
+    def test_factory_honors_configured_container_path(self, base_dir: Path, skills_root: Path, config):
+        config.skills.container_path = "/custom/skills/root"
+        with patch("deerflow.config.paths.get_paths", return_value=Paths(base_dir=base_dir)):
+            with patch("deerflow.config.paths._paths", None):
+                storage = get_or_new_user_skill_storage("test-user", app_config=config)
+        assert storage.get_container_root() == "/custom/skills/root"
+
+    def test_factory_explicit_container_path_wins(self, base_dir: Path, skills_root: Path, config):
+        with patch("deerflow.config.paths.get_paths", return_value=Paths(base_dir=base_dir)):
+            with patch("deerflow.config.paths._paths", None):
+                storage = get_or_new_user_skill_storage("test-user", app_config=config, container_path="/explicit/root")
+        assert storage.get_container_root() == "/explicit/root"
+
+    def test_legacy_visibility_kwargs_branch_seeds_container_path(self, config):
+        """user_should_see_legacy_skills must not fall back to the default root
+        when a caller passes kwargs while a custom root is configured."""
+        config.skills.container_path = "/custom/skills/root"
+        with patch("deerflow.skills.storage.UserScopedSkillStorage") as mock_storage_cls:
+            mock_storage_cls.return_value.load_skills.return_value = []
+            assert user_should_see_legacy_skills("test-user", app_config=config) is False
+        assert mock_storage_cls.call_args.kwargs["container_path"] == "/custom/skills/root"
+
+
 class TestWriteAndRead:
     """Writes go to user dir, reads from user dir when present."""