diff --git a/backend/packages/harness/deerflow/config/agents_config.py b/backend/packages/harness/deerflow/config/agents_config.py
index 0715811a8..7e36b9f2f 100644
--- a/backend/packages/harness/deerflow/config/agents_config.py
+++ b/backend/packages/harness/deerflow/config/agents_config.py
@@ -299,9 +299,32 @@ def load_agent_soul(agent_name: str | None, *, user_id: str | None = None) -> st
     """
     if agent_name:
         agent_dir = resolve_agent_dir(agent_name, user_id=user_id)
+        soul_path = agent_dir / SOUL_FILENAME
+        # Fallback: resolve_agent_dir requires config.yaml to be present
+        # (see #3390), but SOUL.md loading does not depend on config.yaml.
+        # If the resolved dir doesn't have config.yaml (meaning the resolver
+        # returned its default path because no agent dir qualified) and also
+        # lacks SOUL.md, check the per-user and legacy directories directly
+        # so that agents configured via DEER_FLOW_CONFIG_PATH (or any setup
+        # where the agent dir has SOUL.md but no config.yaml) can still load
+        # their soul (#4135). The config.yaml guard ensures this fallback
+        # only fires for dirs the resolver couldn't resolve, not for a
+        # properly-resolved per-user agent that simply lacks SOUL.md -
+        # preserving the "per-user entries fully shadow legacy entries"
+        # invariant (agents_config.py:3-7, list_custom_agents).
+        if not soul_path.exists() and not (agent_dir / "config.yaml").exists():
+            paths = get_paths()
+            effective_user = user_id or get_effective_user_id()
+            for candidate in (
+                paths.user_agent_dir(effective_user, agent_name),
+                paths.agent_dir(agent_name),
+            ):
+                if (candidate / SOUL_FILENAME).exists():
+                    soul_path = candidate / SOUL_FILENAME
+                    break
     else:
         agent_dir = get_paths().base_dir
-    soul_path = agent_dir / SOUL_FILENAME
+        soul_path = agent_dir / SOUL_FILENAME
     if not soul_path.exists():
         return None
     content = soul_path.read_text(encoding="utf-8").strip()
diff --git a/backend/tests/test_custom_agent.py b/backend/tests/test_custom_agent.py
index 0872c529c..f8d34bde6 100644
--- a/backend/tests/test_custom_agent.py
+++ b/backend/tests/test_custom_agent.py
@@ -322,6 +322,73 @@ class TestLoadAgentSoul:
 
         assert soul is None
 
+    def test_loads_soul_without_config_yaml(self, tmp_path):
+        """SOUL.md should load even when the agent dir has no config.yaml (#4135)."""
+        agent_dir = tmp_path / "agents" / "soul-only"
+        agent_dir.mkdir(parents=True)
+        # Deliberately no config.yaml – the agent is configured externally
+        (agent_dir / "SOUL.md").write_text("You are a brave agent.", 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="default"):
+            from deerflow.config.agents_config import load_agent_soul
+
+            soul = load_agent_soul("soul-only")
+
+        assert soul == "You are a brave agent."
+
+    def test_loads_soul_from_user_dir_without_config_yaml(self, tmp_path):
+        """Fallback should find SOUL.md when resolver returns a default dir without it (#4135).
+
+        Setup: per-user agent 'foo' exists as a memory-only directory
+        (no config.yaml, no SOUL.md). Legacy agent 'foo' has SOUL.md but
+        no config.yaml. resolve_agent_dir returns the per-user path as
+        default (neither dir has config.yaml). The fallback then finds
+        SOUL.md in the legacy directory.
+        """
+        # Per-user dir: memory-only (no config.yaml, no SOUL.md)
+        user_dir = tmp_path / "users" / "test-user" / "agents" / "foo"
+        user_dir.mkdir(parents=True)
+        (user_dir / "memory.json").write_text("{}", encoding="utf-8")
+
+        # Legacy dir: has SOUL.md but no config.yaml
+        legacy_dir = tmp_path / "agents" / "foo"
+        legacy_dir.mkdir(parents=True)
+        (legacy_dir / "SOUL.md").write_text("You are a legacy agent.", 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="test-user"):
+            from deerflow.config.agents_config import load_agent_soul
+
+            soul = load_agent_soul("foo")
+
+        assert soul == "You are a legacy agent."
+
+    def test_soul_not_leaked_from_legacy_when_per_user_has_config(self, tmp_path):
+        """Per-user agent with config.yaml but no SOUL.md should NOT fall back to legacy SOUL.md.
+
+        This verifies the gated condition: fallback only fires when the
+        resolved dir lacks config.yaml. A properly-resolved per-user agent
+        that simply has no SOUL.md returns None, preserving the
+        "per-user entries fully shadow legacy entries" invariant.
+        """
+        # Legacy dir: has SOUL.md
+        legacy_dir = tmp_path / "agents" / "foo"
+        legacy_dir.mkdir(parents=True)
+        (legacy_dir / "config.yaml").write_text("name: foo\n")
+        (legacy_dir / "SOUL.md").write_text("You are a legacy agent.", encoding="utf-8")
+
+        # Per-user dir: has config.yaml (resolver returns this) but no SOUL.md
+        user_dir = tmp_path / "users" / "test-user" / "agents" / "foo"
+        user_dir.mkdir(parents=True)
+        (user_dir / "config.yaml").write_text("name: foo\n")
+        # No SOUL.md in per-user dir
+
+        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="test-user"):
+            from deerflow.config.agents_config import load_agent_soul
+
+            soul = load_agent_soul("foo")
+
+        assert soul is None
+
 
 # ===========================================================================
 # 5. list_custom_agents