diff --git a/extensions/matrix/src/matrix/thread-bindings.test.ts b/extensions/matrix/src/matrix/thread-bindings.test.ts
index c872f720832..2b447447c81 100644
--- a/extensions/matrix/src/matrix/thread-bindings.test.ts
+++ b/extensions/matrix/src/matrix/thread-bindings.test.ts
@@ -59,11 +59,12 @@ describe("matrix thread bindings", () => {
     accessToken: "token",
   } as const;
 
-  function resolveBindingsFilePath() {
+  function resolveBindingsFilePath(customStateDir?: string) {
     return path.join(
       resolveMatrixStoragePaths({
         ...auth,
         env: process.env,
+        ...(customStateDir ? { stateDir: customStateDir } : {}),
       }).rootDir,
       "thread-bindings.json",
     );
@@ -432,6 +433,98 @@ describe("matrix thread bindings", () => {
     expect(rotatedBindingsPath).toBe(initialBindingsPath);
   });
 
+  it("replaces reused account managers when the bindings stateDir changes", async () => {
+    const initialStateDir = stateDir;
+    const replacementStateDir = await fs.mkdtemp(
+      path.join(os.tmpdir(), "matrix-thread-bindings-replacement-"),
+    );
+
+    const initialManager = await createMatrixThreadBindingManager({
+      accountId: "ops",
+      auth,
+      client: {} as never,
+      stateDir: initialStateDir,
+      idleTimeoutMs: 24 * 60 * 60 * 1000,
+      maxAgeMs: 0,
+      enableSweeper: false,
+    });
+
+    await getSessionBindingService().bind({
+      targetSessionKey: "agent:ops:subagent:child",
+      targetKind: "subagent",
+      conversation: {
+        channel: "matrix",
+        accountId: "ops",
+        conversationId: "$thread",
+        parentConversationId: "!room:example",
+      },
+      placement: "current",
+    });
+
+    const replacementManager = await createMatrixThreadBindingManager({
+      accountId: "ops",
+      auth,
+      client: {} as never,
+      stateDir: replacementStateDir,
+      idleTimeoutMs: 24 * 60 * 60 * 1000,
+      maxAgeMs: 0,
+      enableSweeper: false,
+    });
+
+    expect(replacementManager).not.toBe(initialManager);
+    expect(replacementManager.listBindings()).toEqual([]);
+    expect(
+      getSessionBindingService().resolveByConversation({
+        channel: "matrix",
+        accountId: "ops",
+        conversationId: "$thread",
+        parentConversationId: "!room:example",
+      }),
+    ).toBeNull();
+
+    await getSessionBindingService().bind({
+      targetSessionKey: "agent:ops:subagent:replacement",
+      targetKind: "subagent",
+      conversation: {
+        channel: "matrix",
+        accountId: "ops",
+        conversationId: "$thread-2",
+        parentConversationId: "!room:example",
+      },
+      placement: "current",
+    });
+
+    await vi.waitFor(async () => {
+      const replacementRaw = await fs.readFile(
+        resolveBindingsFilePath(replacementStateDir),
+        "utf-8",
+      );
+      expect(JSON.parse(replacementRaw)).toMatchObject({
+        version: 1,
+        bindings: [
+          expect.objectContaining({
+            conversationId: "$thread-2",
+            parentConversationId: "!room:example",
+            targetSessionKey: "agent:ops:subagent:replacement",
+          }),
+        ],
+      });
+    });
+    await vi.waitFor(async () => {
+      const initialRaw = await fs.readFile(resolveBindingsFilePath(initialStateDir), "utf-8");
+      expect(JSON.parse(initialRaw)).toMatchObject({
+        version: 1,
+        bindings: [
+          expect.objectContaining({
+            conversationId: "$thread",
+            parentConversationId: "!room:example",
+            targetSessionKey: "agent:ops:subagent:child",
+          }),
+        ],
+      });
+    });
+  });
+
   it("updates lifecycle windows by session key and refreshes activity", async () => {
     vi.useFakeTimers();
     vi.setSystemTime(new Date("2026-03-06T10:00:00.000Z"));
diff --git a/extensions/matrix/src/matrix/thread-bindings.ts b/extensions/matrix/src/matrix/thread-bindings.ts
index fe3116f3691..6cf8029f9e9 100644
--- a/extensions/matrix/src/matrix/thread-bindings.ts
+++ b/extensions/matrix/src/matrix/thread-bindings.ts
@@ -62,7 +62,12 @@ export type MatrixThreadBindingManager = {
   stop: () => void;
 };
 
-const MANAGERS_BY_ACCOUNT_ID = new Map<string, MatrixThreadBindingManager>();
+type MatrixThreadBindingManagerCacheEntry = {
+  filePath: string;
+  manager: MatrixThreadBindingManager;
+};
+
+const MANAGERS_BY_ACCOUNT_ID = new Map<string, MatrixThreadBindingManagerCacheEntry>();
 const BINDINGS_BY_ACCOUNT_CONVERSATION = new Map<string, MatrixThreadBindingRecord>();
 
 function normalizeDurationMs(raw: unknown, fallback: number): number {
@@ -354,17 +359,19 @@ export async function createMatrixThreadBindingManager(params: {
       `Matrix thread binding account mismatch: requested ${params.accountId}, auth resolved ${params.auth.accountId}`,
     );
   }
-  const existing = MANAGERS_BY_ACCOUNT_ID.get(params.accountId);
-  if (existing) {
-    return existing;
-  }
-
   const filePath = resolveBindingsPath({
     auth: params.auth,
     accountId: params.accountId,
     env: params.env,
     stateDir: params.stateDir,
   });
+  const existingEntry = MANAGERS_BY_ACCOUNT_ID.get(params.accountId);
+  if (existingEntry) {
+    if (existingEntry.filePath === filePath) {
+      return existingEntry.manager;
+    }
+    existingEntry.manager.stop();
+  }
   const loaded = await loadBindingsFromDisk(filePath, params.accountId);
   for (const record of loaded) {
     setBindingRecord(record);
@@ -499,7 +506,7 @@ export async function createMatrixThreadBindingManager(params: {
         channel: "matrix",
         accountId: params.accountId,
       });
-      if (MANAGERS_BY_ACCOUNT_ID.get(params.accountId) === manager) {
+      if (MANAGERS_BY_ACCOUNT_ID.get(params.accountId)?.manager === manager) {
         MANAGERS_BY_ACCOUNT_ID.delete(params.accountId);
       }
       for (const record of listBindingsForAccount(params.accountId)) {
@@ -698,14 +705,17 @@ export async function createMatrixThreadBindingManager(params: {
     sweepTimer.unref?.();
   }
 
-  MANAGERS_BY_ACCOUNT_ID.set(params.accountId, manager);
+  MANAGERS_BY_ACCOUNT_ID.set(params.accountId, {
+    filePath,
+    manager,
+  });
   return manager;
 }
 
 export function getMatrixThreadBindingManager(
   accountId: string,
 ): MatrixThreadBindingManager | null {
-  return MANAGERS_BY_ACCOUNT_ID.get(accountId) ?? null;
+  return MANAGERS_BY_ACCOUNT_ID.get(accountId)?.manager ?? null;
 }
 
 export function setMatrixThreadBindingIdleTimeoutBySessionKey(params: {
@@ -713,7 +723,7 @@ export function setMatrixThreadBindingIdleTimeoutBySessionKey(params: {
   targetSessionKey: string;
   idleTimeoutMs: number;
 }): SessionBindingRecord[] {
-  const manager = MANAGERS_BY_ACCOUNT_ID.get(params.accountId);
+  const manager = MANAGERS_BY_ACCOUNT_ID.get(params.accountId)?.manager;
   if (!manager) {
     return [];
   }
@@ -730,7 +740,7 @@ export function setMatrixThreadBindingMaxAgeBySessionKey(params: {
   targetSessionKey: string;
   maxAgeMs: number;
 }): SessionBindingRecord[] {
-  const manager = MANAGERS_BY_ACCOUNT_ID.get(params.accountId);
+  const manager = MANAGERS_BY_ACCOUNT_ID.get(params.accountId)?.manager;
   if (!manager) {
     return [];
   }
@@ -743,7 +753,7 @@ export function setMatrixThreadBindingMaxAgeBySessionKey(params: {
 }
 
 export function resetMatrixThreadBindingsForTests(): void {
-  for (const manager of MANAGERS_BY_ACCOUNT_ID.values()) {
+  for (const { manager } of MANAGERS_BY_ACCOUNT_ID.values()) {
     manager.stop();
   }
   MANAGERS_BY_ACCOUNT_ID.clear();