diff --git a/src/main.ts b/src/main.ts
index 19669f2e5..5908d565f 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -34,7 +34,7 @@ interface RuntimeDependencies {
   readonly serve: typeof serveStdio;
   readonly writeStderr: (text: string) => void;
   readonly setExitCode: (code: number) => void;
-  readonly registerShutdown: (handler: () => void) => void;
+  readonly registerShutdown: (handler: () => void) => () => void;
   readonly registerReload?: (handler: () => void) => () => void;
   readonly createServer?: typeof createServer;
   readonly readProjectPermissionStore?: typeof readProjectPermissionStore;
@@ -52,6 +52,12 @@ const runtimeDependencies = (): RuntimeDependencies => ({
     process.once("SIGTERM", handler);
     process.stdin.once("end", handler);
     process.stdin.once("close", handler);
+    return () => {
+      process.off("SIGINT", handler);
+      process.off("SIGTERM", handler);
+      process.stdin.off("end", handler);
+      process.stdin.off("close", handler);
+    };
   },
   registerReload: (handler) => {
     process.on("SIGHUP", handler);
@@ -232,9 +238,11 @@ export const run = async (
     }) ?? (() => undefined);
 
   let shutdownPromise: Promise<void> | undefined;
+  let unregisterShutdown = (): void => undefined;
   const shutdown = (): Promise<void> => {
     shutdownPromise ??= (async () => {
       unregisterReload();
+      unregisterShutdown();
       await handle.close();
       await session.close();
       permissionAuthority.value.clearSessionGrants();
@@ -249,7 +257,7 @@ export const run = async (
     });
   };
 
-  dependencies.registerShutdown(requestShutdown);
+  unregisterShutdown = dependencies.registerShutdown(requestShutdown);
   return 0;
 };
 
diff --git a/tests/mainErrors.test.ts b/tests/mainErrors.test.ts
index 4b24f61f4..b0ee88447 100644
--- a/tests/mainErrors.test.ts
+++ b/tests/mainErrors.test.ts
@@ -13,18 +13,23 @@ const dependencies = (
   output: string[],
   shutdown: Array<() => void>,
   exitCodes: number[],
+  shutdownUnregistrations: string[] = [],
 ): RuntimeDependencies => ({
   env: {},
   serve,
   writeStderr: (text) => output.push(text),
   setExitCode: (code) => exitCodes.push(code),
-  registerShutdown: (handler) => shutdown.push(handler),
+  registerShutdown: (handler) => {
+    shutdown.push(handler);
+    return () => shutdownUnregistrations.push("shutdown");
+  },
 });
 
 describe("MCP runtime errors", () => {
   it("reports connection loss without the transport cause", async () => {
     const output: string[] = [];
     const shutdown: Array<() => void> = [];
+    const shutdownUnregistrations: string[] = [];
     let options: ServeStdioOptions | undefined;
     let closeCalls = 0;
     const close = (): Promise<void> => {
@@ -42,6 +47,7 @@ describe("MCP runtime errors", () => {
           output,
           shutdown,
           exitCodes,
+          shutdownUnregistrations,
         ),
       ),
     ).toBe(0);
@@ -52,6 +58,42 @@ describe("MCP runtime errors", () => {
     shutdown[0]?.();
     await nextTurn();
     expect(closeCalls).toBe(1);
+    expect(shutdownUnregistrations).toEqual(["shutdown"]);
+  });
+
+  it("unregisters every process-lifetime handler during idempotent shutdown", async () => {
+    const shutdown: Array<() => void> = [];
+    const reload: Array<() => void> = [];
+    const unregistrations: string[] = [];
+    let closeCalls = 0;
+    const runtime: RuntimeDependencies = {
+      ...dependencies(
+        () => ({
+          close: async () => {
+            closeCalls += 1;
+          },
+        }),
+        [],
+        shutdown,
+        [],
+        unregistrations,
+      ),
+      registerReload: (handler) => {
+        reload.push(handler);
+        return () => unregistrations.push("reload");
+      },
+    };
+
+    expect(await run(runtime)).toBe(0);
+    expect(shutdown).toHaveLength(1);
+    expect(reload).toHaveLength(1);
+
+    shutdown[0]?.();
+    shutdown[0]?.();
+    await nextTurn();
+
+    expect(closeCalls).toBe(1);
+    expect(unregistrations).toEqual(["reload", "shutdown"]);
   });
 
   it("reports transport startup failure without its cause", async () => {