diff --git a/backend/packages/harness/deerflow/config/agents_config.py b/backend/packages/harness/deerflow/config/agents_config.py
index 86b5347db..a9c9e212d 100644
--- a/backend/packages/harness/deerflow/config/agents_config.py
+++ b/backend/packages/harness/deerflow/config/agents_config.py
@@ -67,11 +67,13 @@ def resolve_agent_dir(name: str, *, user_id: str | None = None) -> Path:
     paths = get_paths()
     effective_user = user_id or get_effective_user_id()
     user_path = paths.user_agent_dir(effective_user, name)
-    if user_path.exists():
+    # Require config.yaml to confirm this is a genuine agent directory,
+    # not a leftover from memory/storage writes (see #3390).
+    if user_path.exists() and (user_path / "config.yaml").exists():
         return user_path
 
     legacy_path = paths.agent_dir(name)
-    if legacy_path.exists():
+    if legacy_path.exists() and (legacy_path / "config.yaml").exists():
         return legacy_path
 
     return user_path
diff --git a/backend/tests/test_custom_agent.py b/backend/tests/test_custom_agent.py
index 284908081..9f7a61ba2 100644
--- a/backend/tests/test_custom_agent.py
+++ b/backend/tests/test_custom_agent.py
@@ -203,6 +203,79 @@ class TestLoadAgentConfig:
         assert cfg.name == "legacy-agent"
 
 
+# ===========================================================================
+# 3b. resolve_agent_dir — memory-only directory fallback (#3390)
+# ===========================================================================
+
+
+class TestResolveAgentDirMemoryOnlyFallback:
+    """Regression tests for #3390.
+
+    When memory is enabled, the first conversation creates a user-isolated
+    agent directory containing only ``memory.json`` (no ``config.yaml``).
+    On the next turn ``resolve_agent_dir`` must fall through to the legacy
+    shared layout instead of returning the incomplete user directory.
+    """
+
+    def test_user_dir_with_only_memory_falls_back_to_legacy(self, tmp_path):
+        """User dir has memory.json but no config.yaml → use legacy dir."""
+        from deerflow.config.agents_config import resolve_agent_dir
+
+        # Legacy agent with full config
+        legacy_dir = tmp_path / "agents" / "my-agent"
+        legacy_dir.mkdir(parents=True)
+        (legacy_dir / "config.yaml").write_text("name: my-agent\n", encoding="utf-8")
+        (legacy_dir / "SOUL.md").write_text("legacy soul", encoding="utf-8")
+
+        # User dir created by memory write — no config.yaml
+        user_dir = tmp_path / "users" / "u1" / "agents" / "my-agent"
+        user_dir.mkdir(parents=True)
+        (user_dir / "memory.json").write_text("{}", encoding="utf-8")
+
+        with patch("deerflow.config.agents_config.get_paths", return_value=_make_paths(tmp_path)), patch("deerflow.config.agents_config.get_effective_user_id", return_value="u1"):
+            result = resolve_agent_dir("my-agent", user_id="u1")
+
+        assert result == legacy_dir
+
+    def test_user_dir_with_config_takes_priority(self, tmp_path):
+        """User dir with config.yaml should still win over legacy."""
+        from deerflow.config.agents_config import resolve_agent_dir
+
+        # Legacy
+        legacy_dir = tmp_path / "agents" / "my-agent"
+        legacy_dir.mkdir(parents=True)
+        (legacy_dir / "config.yaml").write_text("name: my-agent\n", encoding="utf-8")
+
+        # User dir with full config (migrated)
+        user_dir = tmp_path / "users" / "u1" / "agents" / "my-agent"
+        user_dir.mkdir(parents=True)
+        (user_dir / "config.yaml").write_text("name: my-agent\nmodel: gpt-4\n", encoding="utf-8")
+        (user_dir / "memory.json").write_text("{}", encoding="utf-8")
+
+        with patch("deerflow.config.agents_config.get_paths", return_value=_make_paths(tmp_path)), patch("deerflow.config.agents_config.get_effective_user_id", return_value="u1"):
+            result = resolve_agent_dir("my-agent", user_id="u1")
+
+        assert result == user_dir
+
+    def test_load_config_falls_back_when_user_dir_is_memory_only(self, tmp_path):
+        """End-to-end: load_agent_config works when user dir only has memory.json."""
+        config_dict = {"name": "my-agent", "description": "Legacy agent", "model": "deepseek-v3"}
+        _write_agent(tmp_path, "my-agent", config_dict)
+
+        # Simulate memory write creating user dir without config
+        user_dir = tmp_path / "users" / "u1" / "agents" / "my-agent"
+        user_dir.mkdir(parents=True)
+        (user_dir / "memory.json").write_text("{}", encoding="utf-8")
+
+        with patch("deerflow.config.agents_config.get_paths", return_value=_make_paths(tmp_path)), patch("deerflow.config.agents_config.get_effective_user_id", return_value="u1"):
+            from deerflow.config.agents_config import load_agent_config
+
+            cfg = load_agent_config("my-agent", user_id="u1")
+
+        assert cfg.name == "my-agent"
+        assert cfg.model == "deepseek-v3"
+
+
 # ===========================================================================
 # 4. load_agent_soul
 # ===========================================================================