diff --git a/astrbot/core/agent/tool.py b/astrbot/core/agent/tool.py
index c2536708e6..66c8f2e8f9 100644
--- a/astrbot/core/agent/tool.py
+++ b/astrbot/core/agent/tool.py
@@ -89,11 +89,21 @@ def empty(self) -> bool:
         return len(self.tools) == 0
 
     def add_tool(self, tool: FunctionTool) -> None:
-        """Add a tool to the set."""
-        # 检查是否已存在同名工具
+        """Add a tool to the set.
+
+        If a tool with the same name already exists:
+        - Prefer the one that is active (active=True)
+        - If both have the same active state, use the new one (overwrite)
+        """
         for i, existing_tool in enumerate(self.tools):
             if existing_tool.name == tool.name:
-                self.tools[i] = tool
+                # Use getattr with a default of True for compatibility with tools
+                # that may not define an `active` attribute (e.g., mocks).
+                existing_active = bool(getattr(existing_tool, "active", True))
+                new_active = bool(getattr(tool, "active", True))
+                # Overwrite if new tool is active, or if existing tool is not active
+                if new_active or not existing_active:
+                    self.tools[i] = tool
                 return
         self.tools.append(tool)
 
diff --git a/astrbot/core/provider/func_tool_manager.py b/astrbot/core/provider/func_tool_manager.py
index 068c63c5ad..6f3380abe6 100644
--- a/astrbot/core/provider/func_tool_manager.py
+++ b/astrbot/core/provider/func_tool_manager.py
@@ -311,13 +311,30 @@ def remove_func(self, name: str) -> None:
                 break
 
     def get_func(self, name) -> FuncTool | None:
-        for f in self.func_list:
+        # 优先返回已激活的工具（后加载的覆盖前面的，与 ToolSet.add_tool 保持一致）
+        # 使用 getattr(..., True) 与 ToolSet.add_tool 保持一致：没有 active 属性的工具视为已激活
+        for f in reversed(self.func_list):
+            if f.name == name and getattr(f, "active", True):
+                return f
+        # 退化则拿最后一个同名工具
+        for f in reversed(self.func_list):
             if f.name == name:
                 return f
+        return None
 
     def get_full_tool_set(self) -> ToolSet:
-        """获取完整工具集"""
-        tool_set = ToolSet(self.func_list.copy())
+        """获取完整工具集
+
+        使用 ToolSet.add_tool 进行填充。对于同名工具，去重规则为：
+        - 优先保留 active=True 的工具；
+        - 当 active 状态相同时，后加载的工具会覆盖前面的工具。
+
+        因此，后加载的 inactive 工具不会覆盖已激活的工具；
+        同时，MCP 工具在需要时仍可覆盖被禁用的内置工具。
+        """
+        tool_set = ToolSet()
+        for tool in self.func_list:
+            tool_set.add_tool(tool)
         return tool_set
 
     @staticmethod
diff --git a/tests/unit/test_tool_conflict_resolution.py b/tests/unit/test_tool_conflict_resolution.py
new file mode 100644
index 0000000000..7fd04d4484
--- /dev/null
+++ b/tests/unit/test_tool_conflict_resolution.py
@@ -0,0 +1,233 @@
+"""Tests for tool conflict resolution in ToolSet.add_tool and FunctionToolManager.
+
+This module tests the fix for issue #5821: when an MCP external tool shares a name
+with a disabled built-in tool, the MCP tool should not be removed as collateral damage.
+"""
+
+import pytest
+
+from astrbot.core.agent.tool import FunctionTool, ToolSet
+from astrbot.core.provider.func_tool_manager import FunctionToolManager
+
+
+def make_tool(name: str, active: bool = True) -> FunctionTool:
+    """Create a simple FunctionTool for testing."""
+    return FunctionTool(
+        name=name,
+        description=f"Test tool {name}",
+        parameters={"type": "object", "properties": {}},
+        active=active,
+    )
+
+
+class TestToolSetAddTool:
+    """Tests for ToolSet.add_tool conflict resolution."""
+
+    def test_new_tool_active_existing_inactive_overwrites(self):
+        """Active tool should overwrite inactive tool with same name."""
+        toolset = ToolSet()
+        toolset.add_tool(make_tool("web_search", active=False))
+        toolset.add_tool(make_tool("web_search", active=True))
+
+        assert len(toolset.tools) == 1
+        assert toolset.tools[0].active is True
+
+    def test_new_tool_inactive_existing_active_preserves_existing(self):
+        """Inactive tool should NOT overwrite active tool with same name."""
+        toolset = ToolSet()
+        toolset.add_tool(make_tool("web_search", active=True))
+        toolset.add_tool(make_tool("web_search", active=False))
+
+        assert len(toolset.tools) == 1
+        assert toolset.tools[0].active is True
+
+    def test_both_active_last_one_wins(self):
+        """When both tools are active, the new one should overwrite."""
+        toolset = ToolSet()
+        first = make_tool("web_search", active=True)
+        second = make_tool("web_search", active=True)
+        second.description = "Second web search"
+
+        toolset.add_tool(first)
+        toolset.add_tool(second)
+
+        assert len(toolset.tools) == 1
+        # The second tool should be the one kept
+        assert toolset.tools[0] is second
+        assert toolset.tools[0].description == "Second web search"
+
+    def test_both_inactive_last_one_wins(self):
+        """When both tools are inactive, the new one should overwrite."""
+        toolset = ToolSet()
+        toolset.add_tool(make_tool("web_search", active=False))
+        toolset.add_tool(make_tool("web_search", active=False))
+
+        assert len(toolset.tools) == 1
+
+    def test_different_names_both_added(self):
+        """Tools with different names should both be added."""
+        toolset = ToolSet()
+        toolset.add_tool(make_tool("web_search"))
+        toolset.add_tool(make_tool("code_search"))
+
+        assert len(toolset.tools) == 2
+
+    def test_missing_active_attribute_defaults_to_true(self):
+        """Tools without 'active' attribute should be treated as active."""
+        toolset = ToolSet()
+
+        # Create a mock object without 'active' attribute
+        class MockTool:
+            name = "mock_tool"
+            description = "Mock"
+            parameters = {"type": "object"}
+
+        mock_tool = MockTool()
+        toolset.add_tool(mock_tool)  # type: ignore
+
+        # Should be added successfully
+        assert len(toolset.tools) == 1
+
+        # Adding another tool without active should overwrite
+        mock_tool2 = MockTool()
+        toolset.add_tool(mock_tool2)  # type: ignore
+
+        assert len(toolset.tools) == 1
+
+
+class TestFunctionToolManagerGetFunc:
+    """Tests for FunctionToolManager.get_func with conflict resolution."""
+
+    def test_returns_last_active_tool(self):
+        """Should return the last active tool when multiple have same name."""
+        manager = FunctionToolManager()
+        manager.func_list = [
+            make_tool("web_search", active=True),
+            make_tool("web_search", active=True),
+        ]
+
+        result = manager.get_func("web_search")
+        assert result is not None
+        # Should return the last one (reversed order)
+        assert result is manager.func_list[1]
+
+    def test_returns_active_over_inactive(self):
+        """Should prefer active tool over inactive tool with same name."""
+        manager = FunctionToolManager()
+        manager.func_list = [
+            make_tool("web_search", active=False),
+            make_tool("web_search", active=True),
+        ]
+
+        result = manager.get_func("web_search")
+        assert result is not None
+        assert result.active is True
+        assert result is manager.func_list[1]
+
+    def test_inactive_cannot_override_active(self):
+        """Inactive tool after active should not be returned."""
+        manager = FunctionToolManager()
+        manager.func_list = [
+            make_tool("web_search", active=True),
+            make_tool("web_search", active=False),
+        ]
+
+        result = manager.get_func("web_search")
+        assert result is not None
+        assert result.active is True
+        assert result is manager.func_list[0]
+
+    def test_fallback_to_last_when_none_active(self):
+        """Should return last tool with matching name when none are active."""
+        manager = FunctionToolManager()
+        manager.func_list = [
+            make_tool("web_search", active=False),
+            make_tool("web_search", active=False),
+        ]
+
+        result = manager.get_func("web_search")
+        assert result is not None
+        # Should return the last one (reversed order in fallback)
+        assert result is manager.func_list[1]
+
+    def test_returns_none_when_not_found(self):
+        """Should return None when tool name not found."""
+        manager = FunctionToolManager()
+        manager.func_list = [make_tool("other_tool")]
+
+        result = manager.get_func("web_search")
+        assert result is None
+
+
+class TestFunctionToolManagerGetFullToolSet:
+    """Tests for FunctionToolManager.get_full_tool_set."""
+
+    def test_deduplicates_by_name_using_add_tool(self):
+        """Should deduplicate tools using add_tool logic."""
+        manager = FunctionToolManager()
+        manager.func_list = [
+            make_tool("web_search", active=False),
+            make_tool("web_search", active=True),
+            make_tool("code_search", active=True),
+        ]
+
+        toolset = manager.get_full_tool_set()
+
+        # Should have 2 tools after deduplication
+        assert len(toolset.tools) == 2
+        # web_search should be active (the MCP version)
+        web_search = toolset.get_tool("web_search")
+        assert web_search is not None
+        assert web_search.active is True
+
+    def test_no_deepcopy_preserves_identity(self):
+        """Should not deep copy tools, preserving object identity."""
+        manager = FunctionToolManager()
+        tool = make_tool("web_search")
+        manager.func_list = [tool]
+
+        toolset = manager.get_full_tool_set()
+
+        # Same object reference (no deepcopy)
+        assert toolset.tools[0] is tool
+
+    def test_mcp_tool_overrides_disabled_builtin(self):
+        """
+        Integration test: MCP tool should override disabled built-in tool.
+        This is the core scenario for issue #5821.
+        """
+        manager = FunctionToolManager()
+        # Simulate: built-in tool registered first (disabled)
+        # Then MCP tool registered (enabled)
+        manager.func_list = [
+            make_tool("web_search", active=False),  # Built-in, disabled
+            make_tool("web_search", active=True),  # MCP, enabled
+        ]
+
+        # get_func should return the MCP tool (active one)
+        result = manager.get_func("web_search")
+        assert result is not None
+        assert result.active is True
+        assert result is manager.func_list[1]
+
+        # get_full_tool_set should also keep the MCP tool
+        toolset = manager.get_full_tool_set()
+        assert len(toolset.tools) == 1
+        assert toolset.tools[0].active is True
+
+    def test_disabled_mcp_cannot_override_enabled_builtin(self):
+        """Disabled MCP tool should not override enabled built-in tool."""
+        manager = FunctionToolManager()
+        manager.func_list = [
+            make_tool("web_search", active=True),  # Built-in, enabled
+            make_tool("web_search", active=False),  # MCP, disabled
+        ]
+
+        result = manager.get_func("web_search")
+        assert result is not None
+        assert result.active is True
+        assert result is manager.func_list[0]
+
+        toolset = manager.get_full_tool_set()
+        assert len(toolset.tools) == 1
+        assert toolset.tools[0].active is True