diff --git a/src/features/skill-mcp-manager/connection-race.test.ts b/src/features/skill-mcp-manager/connection-race.test.ts
index 784a3e189..10e3c6836 100644
--- a/src/features/skill-mcp-manager/connection-race.test.ts
+++ b/src/features/skill-mcp-manager/connection-race.test.ts
@@ -248,4 +248,44 @@ describe("getOrCreateClient multi-key disconnect race", () => {
     expect(state.clients.has(clientKey)).toBe(false)
     expect(createdClients[0]?.close).toHaveBeenCalledTimes(1)
   })
+
+  it("#given a superseded pending connection #when a newer client already replaced the map entry #then the stale cleanup does not delete the newer client", async () => {
+    const state = createState()
+    const info = createClientInfo("session-a")
+    const clientKey = createClientKey(info)
+    const pendingConnect = createDeferred<void>()
+    const supersedingConnection = createDeferred<Awaited<ReturnType<typeof getOrCreateClient>>>()
+    pendingConnects.push(pendingConnect)
+
+    const newerClient = new MockClient(
+      { name: "newer-client", version: "1.0.0" },
+      { capabilities: {} },
+    )
+    const newerTransport = new MockStdioClientTransport({ command: "mock-mcp-server" })
+    let replacedEntry = false
+    const originalSet = state.clients.set.bind(state.clients)
+    Reflect.set(state.clients, "set", (key: string, value: SkillMcpManagerState["clients"] extends Map<string, infer TValue> ? TValue : never) => {
+      originalSet(key, value)
+      if (!replacedEntry && key === clientKey) {
+        replacedEntry = true
+        originalSet(key, {
+          client: newerClient as never,
+          transport: newerTransport as never,
+          skillName: info.skillName,
+          lastUsedAt: Date.now(),
+          connectionType: "stdio",
+        })
+      }
+      return state.clients
+    })
+
+    const clientPromise = getOrCreateClient({ state, clientKey, info, config: stdioConfig })
+    state.pendingConnections.set(clientKey, supersedingConnection.promise)
+
+    pendingConnect.resolve(undefined)
+
+    await expect(clientPromise).rejects.toThrow(/superseded by a newer connection attempt/)
+    expect(state.clients.get(clientKey)?.client.close).toBe(newerClient.close)
+    expect(newerClient.close).not.toHaveBeenCalled()
+  })
 })
diff --git a/src/features/skill-mcp-manager/connection.ts b/src/features/skill-mcp-manager/connection.ts
index 3be07d853..890444bce 100644
--- a/src/features/skill-mcp-manager/connection.ts
+++ b/src/features/skill-mcp-manager/connection.ts
@@ -7,6 +7,13 @@ import { createHttpClient } from "./http-client"
 import { createStdioClient } from "./stdio-client"
 import type { SkillMcpClientConnectionParams, SkillMcpClientInfo, SkillMcpManagerState } from "./types"
 
+function removeClientIfCurrent(state: SkillMcpManagerState, clientKey: string, client: Client): void {
+  const managed = state.clients.get(clientKey)
+  if (managed?.client === client) {
+    state.clients.delete(clientKey)
+  }
+}
+
 export async function getOrCreateClient(params: {
   state: SkillMcpManagerState
   clientKey: string
@@ -42,12 +49,13 @@ export async function getOrCreateClient(params: {
 
     const isStale = state.pendingConnections.has(clientKey) && state.pendingConnections.get(clientKey) !== currentConnectionPromise
     if (isStale) {
-      state.clients.delete(clientKey)
+      removeClientIfCurrent(state, clientKey, client)
       try { await client.close() } catch {}
       throw new Error(`Connection for "${info.sessionID}" was superseded by a newer connection attempt.`)
     }
 
     if (state.shutdownGeneration !== shutdownGenAtStart) {
+      removeClientIfCurrent(state, clientKey, client)
       try { await client.close() } catch {}
       throw new Error(`Shutdown occurred during MCP connection for "${info.sessionID}"`)
     }
diff --git a/src/features/skill-mcp-manager/disconnect-cleanup.test.ts b/src/features/skill-mcp-manager/disconnect-cleanup.test.ts
index ab584459b..7c6e2bfb8 100644
--- a/src/features/skill-mcp-manager/disconnect-cleanup.test.ts
+++ b/src/features/skill-mcp-manager/disconnect-cleanup.test.ts
@@ -14,6 +14,8 @@ afterEach(() => {
   trackedStates.length = 0
 })
 
+const expectedCleanupHandlerCount = process.platform === "win32" ? 3 : 2
+
 function createState(): SkillMcpManagerState {
   const state: SkillMcpManagerState = {
     clients: new Map(),
@@ -82,7 +84,7 @@ describe("disconnectSession cleanup registration", () => {
     // then
     expect(state.clients.has("session-2:skill-2:server-2")).toBe(true)
     expect(state.cleanupRegistered).toBe(true)
-    expect(state.cleanupHandlers).toHaveLength(2)
+    expect(state.cleanupHandlers).toHaveLength(expectedCleanupHandlerCount)
     expect(process.listenerCount("SIGINT")).toBe(signalIntCountBeforeRegister + 1)
     expect(process.listenerCount("SIGTERM")).toBe(signalTermCountBeforeRegister + 1)
   })
@@ -124,7 +126,7 @@ describe("disconnectSession cleanup registration", () => {
     expect(state.clients.size).toBe(0)
     expect(state.pendingConnections.size).toBe(1)
     expect(state.cleanupRegistered).toBe(true)
-    expect(state.cleanupHandlers).toHaveLength(2)
+    expect(state.cleanupHandlers).toHaveLength(expectedCleanupHandlerCount)
     expect(process.listenerCount("SIGINT")).toBe(signalIntCountBeforeRegister + 1)
     expect(process.listenerCount("SIGTERM")).toBe(signalTermCountBeforeRegister + 1)
   })