diff --git a/backend/packages/harness/deerflow/config/skills_config.py b/backend/packages/harness/deerflow/config/skills_config.py
index 671b48fde..c306ce747 100644
--- a/backend/packages/harness/deerflow/config/skills_config.py
+++ b/backend/packages/harness/deerflow/config/skills_config.py
@@ -6,6 +6,13 @@ from pydantic import BaseModel, Field
 from deerflow.config.runtime_paths import project_root, resolve_path
 
 
+def _legacy_skills_candidates() -> tuple[Path, ...]:
+    """Return source-tree skills locations for monorepo compatibility."""
+    backend_dir = Path(__file__).resolve().parents[4]
+    repo_root = backend_dir.parent
+    return (repo_root / "skills",)
+
+
 class SkillsConfig(BaseModel):
     """Configuration for skills system"""
 
@@ -15,7 +22,7 @@ class SkillsConfig(BaseModel):
     )
     path: str | None = Field(
         default=None,
-        description="Path to skills directory. If not specified, defaults to skills under the caller project root.",
+        description=("Path to skills directory. If not specified, defaults to `skills` under the caller project root, falling back to the legacy repo-root location for monorepo compatibility."),
     )
     container_path: str = Field(
         default="/mnt/skills",
@@ -26,15 +33,30 @@ class SkillsConfig(BaseModel):
         """
         Get the resolved skills directory path.
 
-        Returns:
-            Path to the skills directory
+        Resolution order:
+            1. Explicit ``path`` field
+            2. ``DEER_FLOW_SKILLS_PATH`` environment variable
+            3. ``skills`` under the caller project root (``project_root()``)
+            4. Legacy repo-root candidates for monorepo compatibility (``_legacy_skills_candidates``)
+
+        When none of (3) or (4) exist on disk, the project-root default is returned so callers
+        can still surface a stable "no skills" location without raising.
         """
         if self.path:
             # Use configured path (can be absolute or relative to project root)
             return resolve_path(self.path)
         if env_path := os.getenv("DEER_FLOW_SKILLS_PATH"):
             return resolve_path(env_path)
-        return project_root() / "skills"
+
+        project_default = project_root() / "skills"
+        if project_default.is_dir():
+            return project_default
+
+        for candidate in _legacy_skills_candidates():
+            if candidate.is_dir():
+                return candidate
+
+        return project_default
 
     def get_skill_container_path(self, skill_name: str, category: str = "public") -> str:
         """
diff --git a/backend/tests/test_runtime_paths.py b/backend/tests/test_runtime_paths.py
index aa9e94641..c6a3d9429 100644
--- a/backend/tests/test_runtime_paths.py
+++ b/backend/tests/test_runtime_paths.py
@@ -7,6 +7,7 @@ import yaml
 
 from deerflow.config import app_config as app_config_module
 from deerflow.config import extensions_config as extensions_config_module
+from deerflow.config import skills_config as skills_config_module
 from deerflow.config.app_config import AppConfig
 from deerflow.config.extensions_config import ExtensionsConfig
 from deerflow.config.paths import Paths
@@ -35,6 +36,7 @@ def test_default_runtime_paths_resolve_from_current_project(tmp_path: Path, monk
         encoding="utf-8",
     )
     (tmp_path / "extensions_config.json").write_text('{"mcpServers": {}, "skills": {}}', encoding="utf-8")
+    (tmp_path / "skills").mkdir()
 
     assert AppConfig.resolve_config_path() == tmp_path / "config.yaml"
     assert ExtensionsConfig.resolve_config_path() == tmp_path / "extensions_config.json"
@@ -121,6 +123,40 @@ def test_app_config_falls_back_to_legacy_when_project_root_lacks_config(tmp_path
     assert AppConfig.resolve_config_path() == legacy_backend_config
 
 
+def test_skills_config_falls_back_to_legacy_when_project_root_lacks_skills(tmp_path: Path, monkeypatch):
+    """When DEER_FLOW_PROJECT_ROOT is unset and cwd has no `skills/`, the legacy
+    repo-root candidate must be used so monorepo runs (cwd=backend/) keep finding
+    `<repo>/skills` instead of `<repo>/backend/skills` (regression test for #2694)."""
+    _clear_path_env(monkeypatch)
+    cwd = tmp_path / "cwd"
+    cwd.mkdir()
+    monkeypatch.chdir(cwd)
+
+    legacy_skills = tmp_path / "legacy-repo" / "skills"
+    legacy_skills.mkdir(parents=True)
+
+    monkeypatch.setattr(
+        skills_config_module,
+        "_legacy_skills_candidates",
+        lambda: (legacy_skills,),
+    )
+
+    assert SkillsConfig().get_skills_path() == legacy_skills
+
+
+def test_skills_config_returns_project_default_when_neither_exists(tmp_path: Path, monkeypatch):
+    """When nothing exists, fall back to the project-root default path so callers
+    surface a stable empty location instead of silently picking a stale legacy dir."""
+    _clear_path_env(monkeypatch)
+    cwd = tmp_path / "cwd"
+    cwd.mkdir()
+    monkeypatch.chdir(cwd)
+
+    monkeypatch.setattr(skills_config_module, "_legacy_skills_candidates", lambda: ())
+
+    assert SkillsConfig().get_skills_path() == cwd / "skills"
+
+
 def test_extensions_config_falls_back_to_legacy_when_project_root_lacks_file(tmp_path: Path, monkeypatch):
     """ExtensionsConfig should hit the legacy backend/repo-root locations when
     the caller project root has no extensions_config.json/mcp_config.json."""
diff --git a/backend/tests/test_skills_loader.py b/backend/tests/test_skills_loader.py
index 886090f71..55b23c68c 100644
--- a/backend/tests/test_skills_loader.py
+++ b/backend/tests/test_skills_loader.py
@@ -19,6 +19,7 @@ def test_get_skills_root_path_points_to_current_project_skills(tmp_path: Path, m
     monkeypatch.delenv("DEER_FLOW_SKILLS_PATH", raising=False)
     monkeypatch.delenv("DEER_FLOW_PROJECT_ROOT", raising=False)
     monkeypatch.chdir(tmp_path)
+    (tmp_path / "skills").mkdir()
 
     app_config = SimpleNamespace(skills=SkillsConfig())
     path = get_or_new_skill_storage(app_config=app_config).get_skills_root_path()