diff --git a/components/apps/src/lib.rs b/components/apps/src/lib.rs
index 2df6ecd3..ac6762f9 100644
--- a/components/apps/src/lib.rs
+++ b/components/apps/src/lib.rs
@@ -349,6 +349,13 @@ impl<R: Runner> Apps<R> {
         // TODO: use CLIENT_ID directly
         let mut filestore = ClientFilestore::new(ADMIN_APP_CLIENT_ID.into(), data.store);
         let version = data.version.encode();
+
+        let valid_migrators = migrations::MIGRATORS;
+        // No migrations if the config failed to load. In that case applications are disabled anyways
+        let config_error_migrators = &[];
+
+        let mut used_migrators = valid_migrators;
+
         let mut app = AdminApp::<R>::load_config(
             trussed,
             &mut filestore,
@@ -356,24 +363,29 @@ impl<R: Runner> Apps<R> {
             version,
             data.version_string,
             data.status(),
-            migrations::MIGRATORS,
+            valid_migrators,
         )
         .unwrap_or_else(|(trussed, _err)| {
             data.init_status.insert(InitStatus::CONFIG_ERROR);
+            used_migrators = config_error_migrators;
             AdminApp::<R>::with_default_config(
                 trussed,
                 runner.uuid(),
                 version,
                 data.version_string,
                 data.status(),
-                // No migrations if the config failed to load. In that case applications are disabled anyways
-                &[],
+                config_error_migrators,
             )
         });
 
-        const LATEST_MIGRATION: u32 = 0;
+        let migration_version = used_migrators
+            .iter()
+            .map(|m| m.version)
+            .max()
+            .unwrap_or_default();
+
         let migration_success = app
-            .migrate(LATEST_MIGRATION, data.store, &mut filestore)
+            .migrate(migration_version, data.store, &mut filestore)
             .is_ok();
         if !migration_success {
             data.init_status.insert(InitStatus::MIGRATION_ERROR);
diff --git a/components/apps/src/migrations.rs b/components/apps/src/migrations.rs
index a72b8419..080f6110 100644
--- a/components/apps/src/migrations.rs
+++ b/components/apps/src/migrations.rs
@@ -7,30 +7,12 @@ pub(crate) const MIGRATION_VERSION_SPACE_EFFICIENCY: u32 = 1;
 
 #[cfg(feature = "backend-auth")]
 pub(crate) const TRUSSED_AUTH_FS_LAYOUT: trussed_auth::FilesystemLayout =
-    trussed_auth::FilesystemLayout::V0;
+    trussed_auth::FilesystemLayout::V1;
 #[cfg(feature = "se050")]
 pub(crate) const SE050_BACKEND_FS_LAYOUT: trussed_se050_backend::FilesystemLayout =
-    trussed_se050_backend::FilesystemLayout::V0;
+    trussed_se050_backend::FilesystemLayout::V1;
 
-/// TODO: When enabling the filesystem layout V1, fido-authenticator will also need to be bump and have its migration enabled
-const _: () = {
-    #[cfg(feature = "backend-auth")]
-    assert!(matches!(
-        TRUSSED_AUTH_FS_LAYOUT,
-        trussed_auth::FilesystemLayout::V0
-    ));
-    #[cfg(feature = "se050")]
-    assert!(matches!(
-        SE050_BACKEND_FS_LAYOUT,
-        trussed_se050_backend::FilesystemLayout::V0
-    ));
-    assert!(MIGRATORS.is_empty());
-};
-
-pub(crate) const MIGRATORS: &[Migrator] = &[];
-
-// TODO: use when enabling migrations of trussed-auth and se050-backend and of fido-authenticator
-const _MIGRATORS: &[Migrator] = &[
+pub(crate) const MIGRATORS: &[Migrator] = &[
     // We first migrate the SE050 since this migration deletes data to make sure that the other
     // migrations succeed even on low block availability
     #[cfg(feature = "se050")]