diff --git a/api/core/app/app_config/easy_ui_based_app/dataset/manager.py b/api/core/app/app_config/easy_ui_based_app/dataset/manager.py
index 3d857a4e9c0..be538455afb 100644
--- a/api/core/app/app_config/easy_ui_based_app/dataset/manager.py
+++ b/api/core/app/app_config/easy_ui_based_app/dataset/manager.py
@@ -213,6 +213,11 @@ class DatasetConfigManager:
             PlanningStrategy.REACT_ROUTER,
         }:
             for tool in config.get("agent_mode", {}).get("tools", []):
+                if not tool:
+                    # Skip malformed empty tool entries; list(tool.keys())[0]
+                    # would otherwise raise IndexError. The sibling convert()
+                    # already guards this with `if len(tool) == 1`.
+                    continue
                 key = list(tool.keys())[0]
                 if key == "dataset":
                     # old style, use tool name as key
diff --git a/api/tests/unit_tests/core/app/app_config/easy_ui_based_app/test_dataset_manager.py b/api/tests/unit_tests/core/app/app_config/easy_ui_based_app/test_dataset_manager.py
index d5305d2fc0b..e4e4f99c6d4 100644
--- a/api/tests/unit_tests/core/app/app_config/easy_ui_based_app/test_dataset_manager.py
+++ b/api/tests/unit_tests/core/app/app_config/easy_ui_based_app/test_dataset_manager.py
@@ -318,3 +318,26 @@ class TestIsDatasetExists:
             return_value=mock_dataset,
         )
         assert not DatasetConfigManager.is_dataset_exists("tenant1", valid_uuid)
+
+
+# ==============================
+# extract_dataset_config_for_legacy_compatibility tests
+# ==============================
+
+
+class TestExtractDatasetConfigForLegacyCompatibility:
+    def test_skips_empty_tool_entry(self):
+        # A malformed empty tool dict in agent_mode.tools must be skipped, not
+        # crash with `IndexError` on `list(tool.keys())[0]`. The sibling
+        # convert() already guards this with `if len(tool) == 1`.
+        config = {
+            "agent_mode": {
+                "enabled": True,
+                "strategy": PlanningStrategy.ROUTER,
+                "tools": [{}],
+            }
+        }
+
+        result = DatasetConfigManager.extract_dataset_config_for_legacy_compatibility("tenant1", AppMode.CHAT, config)
+
+        assert result["agent_mode"]["tools"] == [{}]