diff --git a/src/plugin-handlers/mcp-config-handler-collision.test.ts b/src/plugin-handlers/mcp-config-handler-collision.test.ts
new file mode 100644
index 000000000..1b8de2fa8
--- /dev/null
+++ b/src/plugin-handlers/mcp-config-handler-collision.test.ts
@@ -0,0 +1,132 @@
+/// <reference types="bun-types" />
+
+import { describe, test, expect, spyOn, beforeEach, afterEach } from "bun:test"
+import type { OhMyOpenCodeConfig } from "../config"
+
+import * as mcpLoader from "../features/claude-code-mcp-loader"
+import * as mcpModule from "../mcp"
+import * as shared from "../shared"
+
+let loadMcpConfigsSpy: ReturnType<typeof spyOn>
+let createBuiltinMcpsSpy: ReturnType<typeof spyOn>
+let logSpy: ReturnType<typeof spyOn>
+
+beforeEach(() => {
+  loadMcpConfigsSpy = spyOn(mcpLoader, "loadMcpConfigs").mockResolvedValue({
+    servers: {},
+    loadedServers: [],
+  })
+  createBuiltinMcpsSpy = spyOn(mcpModule, "createBuiltinMcps").mockReturnValue({})
+  logSpy = spyOn(shared, "log").mockImplementation(() => {})
+})
+
+afterEach(() => {
+  loadMcpConfigsSpy.mockRestore()
+  createBuiltinMcpsSpy.mockRestore()
+  logSpy.mockRestore()
+})
+
+function createPluginConfig(overrides: Partial<OhMyOpenCodeConfig> = {}): OhMyOpenCodeConfig {
+  return {
+    disabled_mcps: [],
+    ...overrides,
+  } as OhMyOpenCodeConfig
+}
+
+const EMPTY_PLUGIN_COMPONENTS = {
+  commands: {},
+  skills: {},
+  agents: {},
+  mcpServers: {},
+  hooksConfigs: [],
+  plugins: [],
+  errors: [],
+}
+
+describe("applyMcpConfig collision handling", () => {
+  test("merges without collision when names are unique", async () => {
+    //#given
+    const userMcp = {
+      userServer: { type: "remote", url: "https://user.example.com", enabled: true },
+    }
+
+    loadMcpConfigsSpy.mockResolvedValue({
+      servers: {
+        claudeServer: { type: "remote", url: "https://claude.example.com", enabled: true },
+      },
+      loadedServers: [],
+    })
+
+    const config: Record<string, unknown> = { mcp: userMcp }
+    const pluginConfig = createPluginConfig()
+
+    //#when
+    const { applyMcpConfig } = await import("./mcp-config-handler")
+    await applyMcpConfig({ config, pluginConfig, pluginComponents: EMPTY_PLUGIN_COMPONENTS })
+
+    //#then
+    const mergedMcp = config.mcp as Record<string, Record<string, unknown>>
+    expect(mergedMcp).toHaveProperty("userServer")
+    expect(mergedMcp).toHaveProperty("claudeServer")
+    expect(mergedMcp.userServer.enabled).toBe(true)
+    expect(mergedMcp.claudeServer.enabled).toBe(true)
+    expect(logSpy).not.toHaveBeenCalledWith(expect.stringContaining("overrides Claude Code"))
+  })
+
+  test("user config wins on collision with Claude Code and logs warning", async () => {
+    //#given
+    const userMcp = {
+      sharedServer: { type: "remote", url: "https://user.example.com", enabled: true },
+    }
+
+    loadMcpConfigsSpy.mockResolvedValue({
+      servers: {
+        sharedServer: { type: "remote", url: "https://claude.example.com", enabled: true },
+      },
+      loadedServers: [],
+    })
+
+    const config: Record<string, unknown> = { mcp: userMcp }
+    const pluginConfig = createPluginConfig()
+
+    //#when
+    const { applyMcpConfig } = await import("./mcp-config-handler")
+    await applyMcpConfig({ config, pluginConfig, pluginComponents: EMPTY_PLUGIN_COMPONENTS })
+
+    //#then
+    const mergedMcp = config.mcp as Record<string, Record<string, unknown>>
+    expect(mergedMcp.sharedServer.url).toBe("https://user.example.com")
+    expect(logSpy).toHaveBeenCalledWith(
+      'warning: MCP server "sharedServer" from user config overrides Claude Code .mcp.json'
+    )
+  })
+
+  test("preserves enabled:false from user config after collision with Claude Code", async () => {
+    //#given
+    const userMcp = {
+      sharedServer: { type: "remote", url: "https://user.example.com", enabled: false },
+    }
+
+    loadMcpConfigsSpy.mockResolvedValue({
+      servers: {
+        sharedServer: { type: "remote", url: "https://claude.example.com", enabled: true },
+      },
+      loadedServers: [],
+    })
+
+    const config: Record<string, unknown> = { mcp: userMcp }
+    const pluginConfig = createPluginConfig()
+
+    //#when
+    const { applyMcpConfig } = await import("./mcp-config-handler")
+    await applyMcpConfig({ config, pluginConfig, pluginComponents: EMPTY_PLUGIN_COMPONENTS })
+
+    //#then
+    const mergedMcp = config.mcp as Record<string, Record<string, unknown>>
+    expect(mergedMcp.sharedServer.enabled).toBe(false)
+    expect(mergedMcp.sharedServer.url).toBe("https://user.example.com")
+    expect(logSpy).toHaveBeenCalledWith(
+      'warning: MCP server "sharedServer" from user config overrides Claude Code .mcp.json'
+    )
+  })
+})
diff --git a/src/plugin-handlers/mcp-config-handler.test.ts b/src/plugin-handlers/mcp-config-handler.test.ts
index 95f73fc0d..f9fc6472f 100644
--- a/src/plugin-handlers/mcp-config-handler.test.ts
+++ b/src/plugin-handlers/mcp-config-handler.test.ts
@@ -164,4 +164,5 @@ describe("applyMcpConfig", () => {
     const mergedMcp = config.mcp as Record<string, Record<string, unknown>>
     expect(mergedMcp).not.toHaveProperty("plugin:custom")
   })
+
 })
diff --git a/src/plugin-handlers/mcp-config-handler.ts b/src/plugin-handlers/mcp-config-handler.ts
index d4eef1ad7..82be91942 100644
--- a/src/plugin-handlers/mcp-config-handler.ts
+++ b/src/plugin-handlers/mcp-config-handler.ts
@@ -2,6 +2,7 @@ import type { OhMyOpenCodeConfig } from "../config";
 import { loadMcpConfigs } from "../features/claude-code-mcp-loader";
 import { createBuiltinMcps } from "../mcp";
 import type { PluginComponents } from "./plugin-components-loader";
+import { log } from "../shared";
 
 type McpEntry = Record<string, unknown>;
 
@@ -38,10 +39,18 @@ export async function applyMcpConfig(params: {
     ? await loadMcpConfigs(disabledMcps)
     : { servers: {} };
 
+  if (userMcp) {
+    for (const name of Object.keys(userMcp)) {
+      if (name in mcpResult.servers) {
+        log(`warning: MCP server "${name}" from user config overrides Claude Code .mcp.json`);
+      }
+    }
+  }
+
   const merged = {
     ...createBuiltinMcps(disabledMcps, params.pluginConfig),
-    ...(userMcp ?? {}),
     ...mcpResult.servers,
+    ...(userMcp ?? {}),
     ...params.pluginComponents.mcpServers,
   } as Record<string, McpEntry>;