diff --git a/packages/opencode/src/mcp/index.ts b/packages/opencode/src/mcp/index.ts
index 05f12fa2ee45..175be51276be 100644
--- a/packages/opencode/src/mcp/index.ts
+++ b/packages/opencode/src/mcp/index.ts
@@ -227,7 +227,7 @@ const layer = Layer.effect(
             },
             catch: (e) => (e instanceof Error ? e : new Error(String(e))),
           }),
-        (t, exit) => (Exit.isFailure(exit) ? Effect.tryPromise(() => t.close()).pipe(Effect.ignore) : Effect.void),
+        (t, exit) => (Exit.isFailure(exit) ? stop(t) : Effect.void),
       )
     })
 
@@ -398,11 +398,7 @@ const layer = Layer.effect(
             defs: listed,
             instructions: mcpClient.getInstructions()?.trim(),
           } satisfies CreateResult
-        }).pipe(
-          Effect.catchCause((cause) =>
-            Effect.tryPromise(() => mcpClient.close()).pipe(Effect.ignore, Effect.andThen(Effect.failCause(cause))),
-          ),
-        )
+        }).pipe(Effect.catchCause((cause) => stop(mcpClient).pipe(Effect.andThen(Effect.failCause(cause)))))
       },
       Effect.map((result): CreateResult => result),
       Effect.catchCause((cause) => {
@@ -439,6 +435,59 @@ const layer = Layer.effect(
       Effect.catch(() => Effect.succeed([] as number[])),
     )
 
+    function running(pid: number) {
+      try {
+        process.kill(pid, 0)
+        return true
+      } catch (error) {
+        return !(error instanceof Error && "code" in error && error.code === "ESRCH")
+      }
+    }
+
+    const waitForExit = Effect.fnUntraced(function* (pids: readonly number[], timeout: number) {
+      const deadline = Date.now() + timeout
+      let active = pids.filter(running)
+      while (active.length > 0 && Date.now() < deadline) {
+        yield* Effect.sleep("25 millis")
+        active = active.filter(running)
+      }
+      return active
+    })
+
+    function signal(pids: readonly number[], value: NodeJS.Signals) {
+      for (const pid of pids.toReversed()) {
+        try {
+          process.kill(pid, value)
+        } catch {}
+      }
+    }
+
+    const stop = Effect.fnUntraced(function* (
+      target: MCPClient | StdioClientTransport | TransportWithAuth | undefined,
+    ) {
+      if (!target) return
+      const transport = target instanceof Client ? target.transport : target
+      const root = transport instanceof StdioClientTransport ? transport.pid : null
+      if (typeof root !== "number") {
+        yield* Effect.tryPromise(() => target.close()).pipe(Effect.ignore)
+        return
+      }
+      const children = yield* descendants(root)
+
+      if (children.length > 0) {
+        signal(children, "SIGTERM")
+        signal(yield* waitForExit(children, 500), "SIGKILL")
+      }
+
+      yield* Effect.tryPromise(() => target.close()).pipe(Effect.ignore)
+
+      const known = Array.from(new Set([root, ...children, ...(yield* descendants(root))]))
+      const remaining = yield* waitForExit(known, 250)
+      signal(remaining, "SIGKILL")
+      const survivors = yield* waitForExit(remaining, 1_000)
+      if (survivors.length > 0) yield* Effect.logWarning("MCP processes survived cleanup", { pids: survivors })
+    })
+
     function watch(s: State, name: string, client: MCPClient, bridge: EffectBridge.Shape, timeout?: number) {
       client.onclose = () => {
         if (s.clients[name] !== client) return
@@ -534,23 +583,7 @@ const layer = Layer.effect(
             s.clients = {}
             s.defs = {}
             s.instructions = {}
-            yield* Effect.forEach(
-              clients,
-              (client) =>
-                Effect.gen(function* () {
-                  const pid = client.transport instanceof StdioClientTransport ? client.transport.pid : null
-                  if (typeof pid === "number") {
-                    const pids = yield* descendants(pid)
-                    for (const dpid of pids) {
-                      try {
-                        process.kill(dpid, "SIGTERM")
-                      } catch {}
-                    }
-                  }
-                  yield* Effect.tryPromise(() => client.close()).pipe(Effect.ignore)
-                }),
-              { concurrency: "unbounded" },
-            )
+            yield* Effect.forEach(clients, stop, { concurrency: "unbounded" })
             pendingOAuthTransports.clear()
           }),
         )
@@ -565,7 +598,7 @@ const layer = Layer.effect(
       delete s.defs[name]
       delete s.instructions[name]
       if (!client) return Effect.void
-      return Effect.tryPromise(() => client.close()).pipe(Effect.ignore)
+      return stop(client)
     }
 
     const storeClient = Effect.fnUntraced(function* (
@@ -584,7 +617,7 @@ const layer = Layer.effect(
       if (instructions) s.instructions[name] = instructions
       else delete s.instructions[name]
       watch(s, name, client, bridge, timeout)
-      if (previous) yield* Effect.tryPromise(() => previous.close()).pipe(Effect.ignore)
+      if (previous) yield* stop(previous)
       return s.status[name]
     })
 
@@ -876,9 +909,7 @@ const layer = Layer.effect(
       const result = yield* startAuth(mcpName)
       if (!result.authorizationUrl) {
         const client = "client" in result ? result.client : undefined
-        const mcpConfig = yield* requireMcpConfig(mcpName).pipe(
-          Effect.tapError(() => Effect.tryPromise(() => client?.close() ?? Promise.resolve()).pipe(Effect.ignore)),
-        )
+        const mcpConfig = yield* requireMcpConfig(mcpName).pipe(Effect.tapError(() => stop(client)))
 
         const listed = client
           ? client.getServerCapabilities()?.tools
@@ -886,7 +917,7 @@ const layer = Layer.effect(
             : []
           : undefined
         if (!client || !listed) {
-          yield* Effect.tryPromise(() => client?.close() ?? Promise.resolve()).pipe(Effect.ignore)
+          yield* stop(client)
           return { status: "failed", error: "Failed to get tools" } satisfies Status
         }
 
diff --git a/packages/opencode/test/fixture/mcp-lifecycle-child.mjs b/packages/opencode/test/fixture/mcp-lifecycle-child.mjs
new file mode 100644
index 000000000000..4ce9345d174a
--- /dev/null
+++ b/packages/opencode/test/fixture/mcp-lifecycle-child.mjs
@@ -0,0 +1,24 @@
+import { spawn } from "node:child_process"
+import { writeFileSync } from "node:fs"
+import { fileURLToPath } from "node:url"
+
+const directory = process.env.MCP_LIFECYCLE_DIR
+if (!directory) throw new Error("MCP_LIFECYCLE_DIR is required")
+
+const name = process.argv.includes("--grandchild") ? "grandchild" : "child"
+writeFileSync(`${directory}/${name}.pid`, String(process.pid))
+
+process.on("SIGTERM", () => {
+  writeFileSync(`${directory}/${name}.term`, "received")
+  if (name === "child") process.exit(0)
+})
+
+if (name === "child") {
+  const grandchild = spawn(process.execPath, [fileURLToPath(import.meta.url), "--grandchild"], {
+    env: process.env,
+    stdio: "ignore",
+  })
+  void grandchild
+}
+
+setInterval(() => {}, 60_000)
diff --git a/packages/opencode/test/fixture/mcp-lifecycle-stdio.ts b/packages/opencode/test/fixture/mcp-lifecycle-stdio.ts
index b01ed921cfd4..7c608e082cc8 100644
--- a/packages/opencode/test/fixture/mcp-lifecycle-stdio.ts
+++ b/packages/opencode/test/fixture/mcp-lifecycle-stdio.ts
@@ -1,6 +1,28 @@
 import { Server } from "@modelcontextprotocol/sdk/server/index.js"
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"
 import { ListToolsRequestSchema } from "@modelcontextprotocol/sdk/types.js"
+import { spawn } from "node:child_process"
+
+const lifecycleDir = process.env.MCP_LIFECYCLE_DIR
+const subprocesses: ReturnType<typeof spawn>[] = []
+
+async function waitFor(name: string) {
+  if (!lifecycleDir) throw new Error("MCP_LIFECYCLE_DIR is required")
+  while (!(await Bun.file(`${lifecycleDir}/${name}`).exists())) await Bun.sleep(10)
+}
+
+if (process.argv.includes("--tree")) {
+  if (!lifecycleDir) throw new Error("MCP_LIFECYCLE_DIR is required")
+  await Bun.write(`${lifecycleDir}/parent.pid`, String(process.pid))
+  const node = Bun.which("node")
+  if (!node) throw new Error("node is required for the MCP lifecycle fixture")
+  const subprocess = spawn(node, [`${import.meta.dir}/mcp-lifecycle-child.mjs`, "--child"], {
+    env: process.env,
+    stdio: ["ignore", "ignore", "inherit"],
+  })
+  subprocesses.push(subprocess)
+  await waitFor("grandchild.pid")
+}
 
 if (process.argv.includes("--hang")) {
   const pidFile = process.env.MCP_LIFECYCLE_PID_FILE
@@ -11,8 +33,9 @@ if (process.argv.includes("--hang")) {
 
 const server = new Server({ name: "mcp-lifecycle-stdio", version: "1.0.0" }, { capabilities: { tools: {} } })
 
-server.setRequestHandler(ListToolsRequestSchema, () =>
-  Promise.resolve({
+server.setRequestHandler(ListToolsRequestSchema, () => {
+  if (process.argv.includes("--list-error")) throw new Error("list tools failed")
+  return Promise.resolve({
     tools: [
       {
         name: "current_directory",
@@ -20,7 +43,7 @@ server.setRequestHandler(ListToolsRequestSchema, () =>
         inputSchema: { type: "object", properties: {} },
       },
     ],
-  }),
-)
+  })
+})
 
 await server.connect(new StdioServerTransport())
diff --git a/packages/opencode/test/mcp/lifecycle.test.ts b/packages/opencode/test/mcp/lifecycle.test.ts
index 80c8fd22f886..e6a609af022a 100644
--- a/packages/opencode/test/mcp/lifecycle.test.ts
+++ b/packages/opencode/test/mcp/lifecycle.test.ts
@@ -20,6 +20,7 @@ import { MCP } from "../../src/mcp/index"
 import { McpOAuthCallback } from "../../src/mcp/oauth-callback"
 import { TestInstance } from "../fixture/fixture"
 import { pollWithTimeout, testEffect } from "../lib/effect"
+import { InstanceStore } from "@/project/instance-store"
 
 const it = testEffect(LayerNode.compile(MCP.node))
 const stdioFixture = path.join(import.meta.dir, "../fixture/mcp-lifecycle-stdio.ts")
@@ -182,13 +183,55 @@ function statusName(status: Record<string, MCPNS.Status> | MCPNS.Status, server:
 
 const remote = (url: string, timeout?: number) => ({ type: "remote" as const, url, oauth: false as const, timeout })
 
+const treeFiles = ["parent", "child", "grandchild"] as const
+
+function treeCleanup(directory: string) {
+  return Effect.addFinalizer(() =>
+    Effect.promise(async () => {
+      for (const name of treeFiles) {
+        const file = Bun.file(path.join(directory, `${name}.pid`))
+        if (!(await file.exists())) continue
+        try {
+          process.kill(Number(await file.text()), "SIGKILL")
+        } catch {}
+      }
+    }),
+  )
+}
+
+function readTree(directory: string) {
+  return pollWithTimeout(
+    Effect.promise(async () => {
+      const files = treeFiles.map((name) => Bun.file(path.join(directory, `${name}.pid`)))
+      if (!(await Promise.all(files.map((file) => file.exists()))).every(Boolean)) return
+      return Promise.all(files.map(async (file) => Number(await file.text())))
+    }),
+    "stdio fixture did not publish its process tree",
+  )
+}
+
+function processRunning(pid: number) {
+  try {
+    process.kill(pid, 0)
+    return true
+  } catch {
+    return false
+  }
+}
+
+function waitForTreeExit(pids: readonly number[]) {
+  return pollWithTimeout(
+    Effect.sync(() => (pids.every((pid) => !processRunning(pid)) ? true : undefined)),
+    "stdio fixture process tree was not terminated",
+  )
+}
+
 it.instance("advertises and lists the instance directory as its root", () =>
   Effect.gen(function* () {
     const server = yield* lifecycleServer({ requestRoots: true })
     const mcp = yield* MCP.Service
     const test = yield* TestInstance
     yield* mcp.add("roots", remote(server.url))
-
     const roots = yield* pollWithTimeout(
       Effect.sync(() => server.state.roots),
       "server did not receive roots",
@@ -528,6 +571,99 @@ it.instance("local stdio timeout terminates the real server process", () =>
   }),
 )
 
+if (process.platform !== "win32") {
+  it.instance(
+    "disconnect terminates a real stdio process tree",
+    () =>
+      Effect.gen(function* () {
+        const test = yield* TestInstance
+        yield* treeCleanup(test.directory)
+        const mcp = yield* MCP.Service
+        const result = yield* mcp.add("tree-disconnect", {
+          type: "local",
+          command: [process.execPath, stdioFixture, "--tree"],
+          environment: { MCP_LIFECYCLE_DIR: test.directory },
+        })
+        expect(result.status).toMatchObject({ "tree-disconnect": { status: "connected" } })
+        const pids = yield* readTree(test.directory)
+        expect(pids.every(processRunning)).toBe(true)
+
+        yield* mcp.disconnect("tree-disconnect")
+
+        yield* waitForTreeExit(pids)
+        expect(yield* Effect.promise(() => Bun.file(path.join(test.directory, "grandchild.term")).exists())).toBe(true)
+      }),
+    20_000,
+  )
+
+  it.instance(
+    "replacement terminates only the old stdio process tree",
+    () =>
+      Effect.gen(function* () {
+        const test = yield* TestInstance
+        yield* treeCleanup(test.directory)
+        const mcp = yield* MCP.Service
+        yield* mcp.add("tree-replace", {
+          type: "local",
+          command: [process.execPath, stdioFixture, "--tree"],
+          environment: { MCP_LIFECYCLE_DIR: test.directory },
+        })
+        const pids = yield* readTree(test.directory)
+
+        const result = yield* mcp.add("tree-replace", {
+          type: "local",
+          command: [process.execPath, stdioFixture],
+        })
+
+        expect(statusName(result.status, "tree-replace")).toBe("connected")
+        yield* waitForTreeExit(pids)
+        expect(Object.keys(yield* mcp.tools())).toEqual(["tree-replace_current_directory"])
+      }),
+    20_000,
+  )
+
+  it.instance(
+    "tool discovery failure terminates a real stdio process tree",
+    () =>
+      Effect.gen(function* () {
+        const test = yield* TestInstance
+        yield* treeCleanup(test.directory)
+        const mcp = yield* MCP.Service
+        const result = yield* mcp.add("tree-list-failure", {
+          type: "local",
+          command: [process.execPath, stdioFixture, "--tree", "--list-error"],
+          environment: { MCP_LIFECYCLE_DIR: test.directory },
+        })
+        const pids = yield* readTree(test.directory)
+
+        expect(statusName(result.status, "tree-list-failure")).toBe("failed")
+        yield* waitForTreeExit(pids)
+      }),
+    20_000,
+  )
+
+  it.instance(
+    "instance disposal waits for real stdio process tree cleanup",
+    () =>
+      Effect.gen(function* () {
+        const test = yield* TestInstance
+        yield* treeCleanup(test.directory)
+        const mcp = yield* MCP.Service
+        yield* mcp.add("tree-dispose", {
+          type: "local",
+          command: [process.execPath, stdioFixture, "--tree"],
+          environment: { MCP_LIFECYCLE_DIR: test.directory },
+        })
+        const pids = yield* readTree(test.directory)
+
+        yield* InstanceStore.Service.use((store) => store.disposeDirectory(test.directory))
+
+        yield* waitForTreeExit(pids)
+      }),
+    20_000,
+  )
+}
+
 it.instance("remote timeout aborts both real HTTP transport attempts", () =>
   Effect.gen(function* () {
     const server = yield* hangingLifecycleServer()