diff --git a/apps/server/src/auth/ServerSecretStore.test.ts b/apps/server/src/auth/ServerSecretStore.test.ts
index 08a33e2fde3c5..fa216177f494a 100644
--- a/apps/server/src/auth/ServerSecretStore.test.ts
+++ b/apps/server/src/auth/ServerSecretStore.test.ts
@@ -113,6 +113,55 @@ const layerConcurrentCreateSecretStore = () =>
     Layer.provideMerge(layerConcurrentReadMissFileSystem),
   );
 
+// Both callers read the empty secret before either repairs it, and the second removal of the
+// secret file waits until the first caller has returned its key.
+const layerConcurrentEmptyRepairFileSystem = (firstReturned: Deferred.Deferred<void>) =>
+  Layer.effect(
+    FileSystem.FileSystem,
+    Effect.gen(function* () {
+      const fileSystem = yield* FileSystem.FileSystem;
+      const readCountRef = yield* Ref.make(0);
+      const removeCountRef = yield* Ref.make(0);
+      const readBarrier = yield* Deferred.make<void>();
+      const isSecretPath = (path: string) => /[\\/]session-signing-key\.bin$/.test(path);
+
+      return {
+        ...fileSystem,
+        readFile: (path) =>
+          isSecretPath(path)
+            ? Ref.updateAndGet(readCountRef, (count) => count + 1).pipe(
+                Effect.flatMap((count) =>
+                  count > 2
+                    ? fileSystem.readFile(path)
+                    : Effect.gen(function* () {
+                        if (count === 2) {
+                          yield* Deferred.succeed(readBarrier, void 0);
+                        }
+                        yield* Deferred.await(readBarrier);
+                        return yield* fileSystem.readFile(path);
+                      }),
+                ),
+              )
+            : fileSystem.readFile(path),
+        remove: (path, options) =>
+          isSecretPath(path)
+            ? Ref.updateAndGet(removeCountRef, (count) => count + 1).pipe(
+                Effect.flatMap((count) =>
+                  count > 1 ? Deferred.await(firstReturned) : Effect.void,
+                ),
+                Effect.flatMap(() => fileSystem.remove(path, options)),
+              )
+            : fileSystem.remove(path, options),
+      } satisfies FileSystem.FileSystem;
+    }),
+  ).pipe(Layer.provide(Layer.mergeAll(NodeServices.layer, NodeCrypto.layer)));
+
+const layerConcurrentEmptyRepairSecretStore = (firstReturned: Deferred.Deferred<void>) =>
+  ServerSecretStore.layer.pipe(
+    Layer.provide(layerServerConfig()),
+    Layer.provideMerge(layerConcurrentEmptyRepairFileSystem(firstReturned)),
+  );
+
 it.layer(Layer.mergeAll(NodeServices.layer, NodeCrypto.layer))("ServerSecretStore.layer", (it) => {
   it.effect("reuses an existing secret instead of regenerating it", () =>
     Effect.gen(function* () {
@@ -125,6 +174,40 @@ it.layer(Layer.mergeAll(NodeServices.layer, NodeCrypto.layer))("ServerSecretStor
     }).pipe(Effect.provide(layerServerSecretStore())),
   );
 
+  it.effect("replaces an empty persisted secret with a fresh random one", () =>
+    Effect.gen(function* () {
+      const secretStore = yield* ServerSecretStore.ServerSecretStore;
+      yield* secretStore.set("session-signing-key", new Uint8Array());
+
+      const secret = yield* secretStore.getOrCreateRandom("session-signing-key", 32);
+      const persisted = yield* secretStore.get("session-signing-key");
+
+      assert.equal(secret.byteLength, 32);
+      assert.deepEqual(Array.from(Option.getOrThrow(persisted)), Array.from(secret));
+    }).pipe(Effect.provide(layerServerSecretStore())),
+  );
+
+  it.effect("keeps the repaired secret when concurrent callers find it empty", () =>
+    Effect.gen(function* () {
+      const firstReturned = yield* Deferred.make<void>();
+      yield* Effect.gen(function* () {
+        const secretStore = yield* ServerSecretStore.ServerSecretStore;
+        yield* secretStore.set("session-signing-key", new Uint8Array());
+        const getOrCreate = secretStore
+          .getOrCreateRandom("session-signing-key", 32)
+          .pipe(Effect.tap(() => Deferred.succeed(firstReturned, void 0)));
+
+        const [first, second] = yield* Effect.all([getOrCreate, getOrCreate], {
+          concurrency: "unbounded",
+        });
+        const persisted = Option.getOrThrow(yield* secretStore.get("session-signing-key"));
+
+        assert.deepEqual(Array.from(first), Array.from(persisted));
+        assert.deepEqual(Array.from(second), Array.from(persisted));
+      }).pipe(Effect.provide(layerConcurrentEmptyRepairSecretStore(firstReturned)));
+    }),
+  );
+
   it.effect("returns the persisted secret when concurrent creators race", () =>
     Effect.gen(function* () {
       const secretStore = yield* ServerSecretStore.ServerSecretStore;
diff --git a/apps/server/src/auth/ServerSecretStore.ts b/apps/server/src/auth/ServerSecretStore.ts
index e950acb38a71d..cabded3d0c7b0 100644
--- a/apps/server/src/auth/ServerSecretStore.ts
+++ b/apps/server/src/auth/ServerSecretStore.ts
@@ -8,6 +8,7 @@ import * as Path from "effect/Path";
 import * as Predicate from "effect/Predicate";
 import * as PlatformError from "effect/PlatformError";
 import * as Schema from "effect/Schema";
+import * as Semaphore from "effect/Semaphore";
 
 import * as ServerConfig from "../config.ts";
 
@@ -169,6 +170,9 @@ export const make = Effect.gen(function* () {
   );
 
   const resolveSecretPath = (name: string) => path.join(serverConfig.secretsDir, `${name}.bin`);
+  const emptySecretRepair = yield* Semaphore.make(1);
+  const isMissingOrNonEmpty = (secret: Option.Option<Uint8Array>) =>
+    Option.isNone(secret) || secret.value.byteLength > 0;
 
   const get: ServerSecretStore["Service"]["get"] = (name) =>
     fileSystem.readFile(resolveSecretPath(name)).pipe(
@@ -263,6 +267,19 @@ export const make = Effect.gen(function* () {
 
   const getOrCreateRandom: ServerSecretStore["Service"]["getOrCreateRandom"] = (name, bytes) =>
     get(name).pipe(
+      // Older builds could persist a 0-byte secret, which is never a usable key. Re-read under
+      // the permit, and keep it until an interrupted removal settles, so a caller that saw the
+      // empty file cannot remove a key another caller created.
+      Effect.filterOrElse(isMissingOrNonEmpty, () =>
+        emptySecretRepair.withPermits(1)(
+          get(name).pipe(
+            Effect.filterOrElse(isMissingOrNonEmpty, () =>
+              remove(name).pipe(Effect.as(Option.none<Uint8Array>())),
+            ),
+            Effect.uninterruptible,
+          ),
+        ),
+      ),
       Effect.flatMap(
         Option.match({
           onSome: Effect.succeed,