diff --git a/extensions/matrix/src/matrix/client/logging.ts b/extensions/matrix/src/matrix/client/logging.ts
index a260aab4619..386ca295eb6 100644
--- a/extensions/matrix/src/matrix/client/logging.ts
+++ b/extensions/matrix/src/matrix/client/logging.ts
@@ -1,12 +1,8 @@
-import { logger as matrixJsSdkRootLogger } from "matrix-js-sdk/lib/logger.js";
 import { ConsoleLogger, LogService, setMatrixConsoleLogging } from "../sdk/logger.js";
 
 let matrixSdkLoggingConfigured = false;
 let matrixSdkLogMode: "default" | "quiet" = "default";
 const matrixSdkBaseLogger = new ConsoleLogger();
-const matrixSdkSilentMethodFactory = () => () => {};
-let matrixSdkRootMethodFactory: unknown;
-let matrixSdkRootLoggerInitialized = false;
 
 type MatrixJsSdkLogger = {
   trace: (...messageOrObject: unknown[]) => void;
@@ -52,22 +48,7 @@ export function createMatrixJsSdkClientLogger(prefix = "matrix"): MatrixJsSdkLog
   return createMatrixJsSdkLoggerInstance(prefix);
 }
 
-function applyMatrixJsSdkRootLoggerMode(): void {
-  const rootLogger = matrixJsSdkRootLogger as {
-    methodFactory?: unknown;
-    rebuild?: () => void;
-  };
-  if (!matrixSdkRootLoggerInitialized) {
-    matrixSdkRootMethodFactory = rootLogger.methodFactory;
-    matrixSdkRootLoggerInitialized = true;
-  }
-  rootLogger.methodFactory =
-    matrixSdkLogMode === "quiet" ? matrixSdkSilentMethodFactory : matrixSdkRootMethodFactory;
-  rootLogger.rebuild?.();
-}
-
 function applyMatrixSdkLogger(): void {
-  applyMatrixJsSdkRootLoggerMode();
   if (matrixSdkLogMode === "quiet") {
     LogService.setLogger({
       trace: () => {},
diff --git a/extensions/matrix/src/matrix/sdk.test.ts b/extensions/matrix/src/matrix/sdk.test.ts
index d54b2855131..90e8de38ab6 100644
--- a/extensions/matrix/src/matrix/sdk.test.ts
+++ b/extensions/matrix/src/matrix/sdk.test.ts
@@ -1404,6 +1404,26 @@ describe("MatrixClient crypto bootstrapping", () => {
     expect(logger?.getChild).toBeTypeOf("function");
   });
 
+  it("passes a custom sync filter to matrix-js-sdk startup", async () => {
+    const client = new MatrixClient("https://matrix.example.org", "token", {
+      userId: "@bot:example.org",
+      syncFilter: { room: { ephemeral: { not_types: ["m.receipt"] } } },
+    });
+
+    await client.start();
+
+    const startOpts = matrixJsClient.startClient.mock.calls[0]?.[0] as
+      | { filter?: { getDefinition?: () => unknown } }
+      | undefined;
+    expect(startOpts?.filter?.getDefinition?.()).toEqual({
+      room: {
+        ephemeral: {
+          not_types: ["m.receipt"],
+        },
+      },
+    });
+  });
+
   it("schedules periodic crypto snapshot persistence with fake timers", async () => {
     vi.useFakeTimers();
     const databasesSpy = vi.spyOn(indexedDB, "databases").mockResolvedValue([]);
diff --git a/extensions/matrix/src/matrix/sdk.ts b/extensions/matrix/src/matrix/sdk.ts
index 59d9b11a1c9..3259af650a5 100644
--- a/extensions/matrix/src/matrix/sdk.ts
+++ b/extensions/matrix/src/matrix/sdk.ts
@@ -1,9 +1,11 @@
 import { EventEmitter } from "node:events";
 import {
   ClientEvent,
+  Filter,
   MatrixEventEvent,
   Preset,
   createClient as createMatrixJsClient,
+  type IFilterDefinition,
   type MatrixClient as MatrixJsClient,
   type MatrixEvent,
 } from "matrix-js-sdk/lib/matrix.js";
@@ -216,6 +218,7 @@ export class MatrixClient {
   private readonly httpClient: MatrixAuthedHttpClient;
   private readonly localTimeoutMs: number;
   private readonly initialSyncLimit?: number;
+  private readonly syncFilter?: IFilterDefinition;
   private readonly encryptionEnabled: boolean;
   private readonly password?: string;
   private readonly syncStore?: FileBackedMatrixSyncStore;
@@ -258,6 +261,7 @@ export class MatrixClient {
       localTimeoutMs?: number;
       encryption?: boolean;
       initialSyncLimit?: number;
+      syncFilter?: IFilterDefinition;
       storagePath?: string;
       recoveryKeyPath?: string;
       idbSnapshotPath?: string;
@@ -275,6 +279,7 @@ export class MatrixClient {
     });
     this.localTimeoutMs = Math.max(1, opts.localTimeoutMs ?? 60_000);
     this.initialSyncLimit = opts.initialSyncLimit;
+    this.syncFilter = opts.syncFilter;
     this.encryptionEnabled = opts.encryption === true;
     this.password = opts.password;
     this.syncStore = opts.storagePath ? new FileBackedMatrixSyncStore(opts.storagePath) : undefined;
@@ -496,6 +501,7 @@ export class MatrixClient {
 
     await this.client.startClient({
       initialSyncLimit: this.initialSyncLimit,
+      ...(this.syncFilter ? { filter: Filter.fromJson(this.selfUserId, "", this.syncFilter) } : {}),
     });
     await this.waitForInitialSyncReady({
       abortSignal: opts.abortSignal,
@@ -1674,6 +1680,12 @@ export class MatrixClient {
       "MatrixClientLite",
       "No room key backup version found on server, creating one via secret storage bootstrap",
     );
+    // matrix-js-sdk 41.3.0 can log a transient PerSessionKeyBackupDownloader
+    // "current backup version ... undefined" warning while setupNewKeyBackup creates
+    // the backup: resetKeyBackup emits key-backup cache events before its async
+    // checkKeyBackupAndEnable pass has populated active backup state. Keep the
+    // explicit server re-check below and do not hide the SDK logs; if this needs
+    // fixing in code, upstream a minimal Matrix SDK repro instead of patching here.
     await this.recoveryKeyStore.bootstrapSecretStorageWithRecoveryKey(crypto, {
       setupNewKeyBackup: true,
     });
diff --git a/extensions/matrix/src/matrix/sdk/crypto-bootstrap.test.ts b/extensions/matrix/src/matrix/sdk/crypto-bootstrap.test.ts
index 99db1115302..accacfb7ecc 100644
--- a/extensions/matrix/src/matrix/sdk/crypto-bootstrap.test.ts
+++ b/extensions/matrix/src/matrix/sdk/crypto-bootstrap.test.ts
@@ -222,6 +222,26 @@ describe("MatrixCryptoBootstrapper", () => {
     );
   });
 
+  it("refreshes published cross-signing keys before importing private keys from secret storage", async () => {
+    const bootstrapCrossSigning = vi.fn(async () => {});
+    const userHasCrossSigningKeys = vi.fn(async () => true);
+    const { bootstrapper, crypto } = createBootstrapperHarness({
+      bootstrapCrossSigning,
+      getDeviceVerificationStatus: vi.fn(async () => createVerifiedDeviceStatus()),
+      isCrossSigningReady: vi.fn(async () => true),
+      userHasCrossSigningKeys,
+    });
+
+    await bootstrapper.bootstrap(crypto, {
+      allowAutomaticCrossSigningReset: false,
+    });
+
+    expect(userHasCrossSigningKeys).toHaveBeenCalledWith("@bot:example.org", true);
+    expect(userHasCrossSigningKeys.mock.invocationCallOrder[0]).toBeLessThan(
+      bootstrapCrossSigning.mock.invocationCallOrder[0],
+    );
+  });
+
   it("passes explicit secret-storage repair allowance only when requested", async () => {
     const deps = createBootstrapperDeps();
     const crypto = createCryptoApi({
diff --git a/extensions/matrix/src/matrix/sdk/crypto-bootstrap.ts b/extensions/matrix/src/matrix/sdk/crypto-bootstrap.ts
index 3686800c626..cbcd942dabe 100644
--- a/extensions/matrix/src/matrix/sdk/crypto-bootstrap.ts
+++ b/extensions/matrix/src/matrix/sdk/crypto-bootstrap.ts
@@ -142,6 +142,16 @@ export class MatrixCryptoBootstrapper<TRawEvent extends MatrixRawEvent> {
         return false;
       }
     };
+    const refreshPublishedCrossSigningKeys = async (): Promise<void> => {
+      if (typeof crypto.userHasCrossSigningKeys !== "function") {
+        return;
+      }
+      try {
+        await crypto.userHasCrossSigningKeys(userId, true);
+      } catch {
+        // The normal bootstrap flow below handles missing or unavailable keys.
+      }
+    };
     const isCrossSigningReady = async (): Promise<boolean> => {
       if (typeof crypto.isCrossSigningReady !== "function") {
         return true;
@@ -212,6 +222,7 @@ export class MatrixCryptoBootstrapper<TRawEvent extends MatrixRawEvent> {
 
     // First pass: preserve existing cross-signing identity and ensure public keys are uploaded.
     try {
+      await refreshPublishedCrossSigningKeys();
       await crypto.bootstrapCrossSigning({
         authUploadDeviceSigningKeys,
       });