diff --git a/Jellyfin.Server/Migrations/MigrationRunner.cs b/Jellyfin.Server/Migrations/MigrationRunner.cs
index c3a2e1bc4e..c223576dad 100644
--- a/Jellyfin.Server/Migrations/MigrationRunner.cs
+++ b/Jellyfin.Server/Migrations/MigrationRunner.cs
@@ -149,11 +149,18 @@ namespace Jellyfin.Server.Migrations
                 }
             }
 
+            List<IMigrationRoutine> databaseMigrations = [];
             try
             {
                 foreach (var migrationRoutine in migrationsToBeApplied)
                 {
                     logger.LogInformation("Applying migration '{Name}'", migrationRoutine.Name);
+                    var isDbMigration = migrationRoutine is IDatabaseMigrationRoutine;
+
+                    if (isDbMigration)
+                    {
+                        databaseMigrations.Add(migrationRoutine);
+                    }
 
                     try
                     {
@@ -167,17 +174,31 @@ namespace Jellyfin.Server.Migrations
 
                     // Mark the migration as completed
                     logger.LogInformation("Migration '{Name}' applied successfully", migrationRoutine.Name);
-                    migrationOptions.Applied.Add((migrationRoutine.Id, migrationRoutine.Name));
-                    saveConfiguration(migrationOptions);
-                    logger.LogDebug("Migration '{Name}' marked as applied in configuration.", migrationRoutine.Name);
+                    if (!isDbMigration)
+                    {
+                        migrationOptions.Applied.Add((migrationRoutine.Id, migrationRoutine.Name));
+                        saveConfiguration(migrationOptions);
+                        logger.LogDebug("Migration '{Name}' marked as applied in configuration.", migrationRoutine.Name);
+                    }
                 }
             }
-            catch (System.Exception) when (migrationKey is not null && jellyfinDatabaseProvider is not null)
+            catch (Exception) when (migrationKey is not null && jellyfinDatabaseProvider is not null)
             {
-                logger.LogInformation("Rollback on database as migration reported failure.");
-                await jellyfinDatabaseProvider.RestoreBackupFast(migrationKey, CancellationToken.None).ConfigureAwait(false);
+                if (databaseMigrations.Count != 0)
+                {
+                    logger.LogInformation("Rolling back database as migrations reported failure.");
+                    await jellyfinDatabaseProvider.RestoreBackupFast(migrationKey, CancellationToken.None).ConfigureAwait(false);
+                }
+
                 throw;
             }
+
+            foreach (var migrationRoutine in databaseMigrations)
+            {
+                migrationOptions.Applied.Add((migrationRoutine.Id, migrationRoutine.Name));
+                saveConfiguration(migrationOptions);
+                logger.LogDebug("Migration '{Name}' marked as applied in configuration.", migrationRoutine.Name);
+            }
         }
     }
 }
diff --git a/src/Jellyfin.Database/Jellyfin.Database.Providers.Sqlite/SqliteDatabaseProvider.cs b/src/Jellyfin.Database/Jellyfin.Database.Providers.Sqlite/SqliteDatabaseProvider.cs
index e818c3524a..bd5631074f 100644
--- a/src/Jellyfin.Database/Jellyfin.Database.Providers.Sqlite/SqliteDatabaseProvider.cs
+++ b/src/Jellyfin.Database/Jellyfin.Database.Providers.Sqlite/SqliteDatabaseProvider.cs
@@ -98,7 +98,7 @@ public sealed class SqliteDatabaseProvider : IJellyfinDatabaseProvider
             Directory.CreateDirectory(backupFile);
         }
 
-        backupFile = Path.Combine(_applicationPaths.DataPath, $"{key}_jellyfin.db");
+        backupFile = Path.Combine(backupFile, $"{key}_jellyfin.db");
         File.Copy(path, backupFile);
         return Task.FromResult(key);
     }
@@ -106,6 +106,8 @@ public sealed class SqliteDatabaseProvider : IJellyfinDatabaseProvider
     /// <inheritdoc />
     public Task RestoreBackupFast(string key, CancellationToken cancellationToken)
     {
+        // ensure there are absolutly no dangling Sqlite connections.
+        SqliteConnection.ClearAllPools();
         var path = Path.Combine(_applicationPaths.DataPath, "jellyfin.db");
         var backupFile = Path.Combine(_applicationPaths.DataPath, BackupFolderName, $"{key}_jellyfin.db");