diff --git a/Jellyfin.Server/CoreAppHost.cs b/Jellyfin.Server/CoreAppHost.cs
index cd5a2ce853..8b4b61e290 100644
--- a/Jellyfin.Server/CoreAppHost.cs
+++ b/Jellyfin.Server/CoreAppHost.cs
@@ -57,33 +57,5 @@ namespace Jellyfin.Server
 
         /// <inheritdoc />
         protected override void ShutdownInternal() => Program.Shutdown();
-
-        /// <summary>
-        /// Runs the migration routines if necessary.
-        /// </summary>
-        public void TryMigrate()
-        {
-            var previousVersion = ConfigurationManager.CommonConfiguration.PreviousVersion;
-            switch (ApplicationVersion.CompareTo(previousVersion))
-            {
-                case 1:
-                    Logger.LogWarning("Version check shows Jellyfin was updated: previous version={0}, current version={1}", previousVersion, ApplicationVersion);
-
-                    Migrations.Run(this, Logger);
-
-                    ConfigurationManager.CommonConfiguration.PreviousVersion = ApplicationVersion;
-                    ConfigurationManager.SaveConfiguration();
-                    break;
-                case 0:
-                    // nothing to do, versions match
-                    break;
-                case -1:
-                    Logger.LogWarning("Version check shows Jellyfin was rolled back, use at your own risk: previous version={0}, current version={1}", previousVersion, ApplicationVersion);
-                    // no "rollback" routines for now
-                    ConfigurationManager.CommonConfiguration.PreviousVersion = ApplicationVersion;
-                    ConfigurationManager.SaveConfiguration();
-                    break;
-            }
-        }
     }
 }
diff --git a/Jellyfin.Server/Migrations.cs b/Jellyfin.Server/Migrations.cs
deleted file mode 100644
index 95fea4ea55..0000000000
--- a/Jellyfin.Server/Migrations.cs
+++ /dev/null
@@ -1,92 +0,0 @@
-using System;
-using System.Collections.Generic;
-using MediaBrowser.Common.Configuration;
-using MediaBrowser.Model.Configuration;
-using Microsoft.Extensions.Logging;
-
-namespace Jellyfin.Server
-{
-    /// <summary>
-    /// The class that knows how migrate between different Jellyfin versions.
-    /// </summary>
-    internal static class Migrations
-    {
-        private static readonly IUpdater[] _migrations =
-        {
-            new Pre10_5()
-        };
-
-        /// <summary>
-        /// Interface that descibes a migration routine.
-        /// </summary>
-        private interface IUpdater
-        {
-            /// <summary>
-            /// Gets maximum version this Updater applies to.
-            /// If current version is greater or equal to it, skip the updater.
-            /// </summary>
-            public abstract Version Maximum { get; }
-
-            /// <summary>
-            /// Execute the migration from version "from".
-            /// </summary>
-            /// <param name="host">Host that hosts current version.</param>
-            /// <param name="logger">Host logger.</param>
-            /// <param name="from">Version to migrate from.</param>
-            /// <returns>Whether configuration was changed.</returns>
-            public abstract bool Perform(CoreAppHost host, ILogger logger, Version from);
-        }
-
-        /// <summary>
-        /// Run all needed migrations.
-        /// </summary>
-        /// <param name="host">CoreAppHost that hosts current version.</param>
-        /// <param name="logger">AppHost logger.</param>
-        /// <returns>Whether anything was changed.</returns>
-        public static bool Run(CoreAppHost host, ILogger logger)
-        {
-            bool updated = false;
-            var version = host.ServerConfigurationManager.CommonConfiguration.PreviousVersion;
-
-            for (var i = 0; i < _migrations.Length; i++)
-            {
-                var updater = _migrations[i];
-                if (version.CompareTo(updater.Maximum) >= 0)
-                {
-                    logger.LogDebug("Skipping updater {0} as current version {1} >= its maximum applicable version {2}", updater, version, updater.Maximum);
-                    continue;
-                }
-
-                if (updater.Perform(host, logger, version))
-                {
-                    updated = true;
-                }
-
-                version = updater.Maximum;
-            }
-
-            return updated;
-        }
-
-        private class Pre10_5 : IUpdater
-        {
-            public Version Maximum { get => Version.Parse("10.5.0"); }
-
-            public bool Perform(CoreAppHost host, ILogger logger, Version from)
-            {
-                // Set EnableThrottling to false as it wasn't used before, and in 10.5.0 it may introduce issues
-                var encoding = ((IConfigurationManager)host.ServerConfigurationManager).GetConfiguration<EncodingOptions>("encoding");
-                if (encoding.EnableThrottling)
-                {
-                    logger.LogInformation("Disabling transcoding throttling during migration");
-                    encoding.EnableThrottling = false;
-
-                    host.ServerConfigurationManager.SaveConfiguration("encoding", encoding);
-                    return true;
-                }
-
-                return false;
-            }
-        }
-    }
-}
diff --git a/Jellyfin.Server/Migrations/IUpdater.cs b/Jellyfin.Server/Migrations/IUpdater.cs
new file mode 100644
index 0000000000..9b749841cf
--- /dev/null
+++ b/Jellyfin.Server/Migrations/IUpdater.cs
@@ -0,0 +1,23 @@
+using System;
+using Microsoft.Extensions.Logging;
+
+namespace Jellyfin.Server.Migrations
+{
+    /// <summary>
+    /// Interface that descibes a migration routine.
+    /// </summary>
+    internal interface IUpdater
+    {
+        /// <summary>
+        /// Gets the name of the migration, must be unique.
+        /// </summary>
+        public abstract string Name { get; }
+
+        /// <summary>
+        /// Execute the migration routine.
+        /// </summary>
+        /// <param name="host">Host that hosts current version.</param>
+        /// <param name="logger">Host logger.</param>
+        public abstract void Perform(CoreAppHost host, ILogger logger);
+    }
+}
diff --git a/Jellyfin.Server/Migrations/MigrationOptions.cs b/Jellyfin.Server/Migrations/MigrationOptions.cs
new file mode 100644
index 0000000000..6b7831158f
--- /dev/null
+++ b/Jellyfin.Server/Migrations/MigrationOptions.cs
@@ -0,0 +1,23 @@
+namespace Jellyfin.Server.Migrations
+{
+    /// <summary>
+    /// Configuration part that holds all migrations that were applied.
+    /// </summary>
+    public class MigrationOptions
+    {
+        /// <summary>
+        /// Initializes a new instance of the <see cref="MigrationOptions"/> class.
+        /// </summary>
+        public MigrationOptions()
+        {
+            Applied = System.Array.Empty<string>();
+        }
+
+#pragma warning disable CA1819 // Properties should not return arrays
+        /// <summary>
+        /// Gets or sets the list of applied migration routine names.
+        /// </summary>
+        public string[] Applied { get; set; }
+#pragma warning restore CA1819 // Properties should not return arrays
+    }
+}
diff --git a/Jellyfin.Server/Migrations/MigrationRunner.cs b/Jellyfin.Server/Migrations/MigrationRunner.cs
new file mode 100644
index 0000000000..ca4c79cfd3
--- /dev/null
+++ b/Jellyfin.Server/Migrations/MigrationRunner.cs
@@ -0,0 +1,75 @@
+using System;
+using System.Linq;
+using MediaBrowser.Common.Configuration;
+using Microsoft.Extensions.Logging;
+
+namespace Jellyfin.Server.Migrations
+{
+    /// <summary>
+    /// The class that knows which migrations to apply and how to apply them.
+    /// </summary>
+    public sealed class MigrationRunner
+    {
+        /// <summary>
+        /// The list of known migrations, in order of applicability.
+        /// </summary>
+        internal static readonly IUpdater[] Migrations =
+        {
+            new Routines.DisableTranscodingThrottling()
+        };
+
+        /// <summary>
+        /// Run all needed migrations.
+        /// </summary>
+        /// <param name="host">CoreAppHost that hosts current version.</param>
+        /// <param name="loggerFactory">Factory for making the logger.</param>
+        public static void Run(CoreAppHost host, ILoggerFactory loggerFactory)
+        {
+            var logger = loggerFactory.CreateLogger<MigrationRunner>();
+            var migrationOptions = ((IConfigurationManager)host.ServerConfigurationManager).GetConfiguration<MigrationOptions>(MigrationsListStore.StoreKey);
+
+            if (!host.ServerConfigurationManager.Configuration.IsStartupWizardCompleted && migrationOptions.Applied.Length == 0)
+            {
+                // If startup wizard is not finished, this is a fresh install.
+                // Don't run any migrations, just mark all of them as applied.
+                logger.LogInformation("Marking all known migrations as applied because this is fresh install");
+                migrationOptions.Applied = Migrations.Select(m => m.Name).ToArray();
+                host.ServerConfigurationManager.SaveConfiguration(MigrationsListStore.StoreKey, migrationOptions);
+                return;
+            }
+
+            var applied = migrationOptions.Applied.ToList();
+
+            for (var i = 0; i < Migrations.Length; i++)
+            {
+                var updater = Migrations[i];
+                if (applied.Contains(updater.Name))
+                {
+                    logger.LogDebug("Skipping migration '{Name}' since it is already applied", updater.Name);
+                    continue;
+                }
+
+                logger.LogInformation("Applying migration '{Name}'", updater.Name);
+                try
+                {
+                    updater.Perform(host, logger);
+                }
+                catch (Exception ex)
+                {
+                    logger.LogError(ex, "Could not apply migration '{Name}'", updater.Name);
+                    throw;
+                }
+
+                logger.LogInformation("Migration '{Name}' applied successfully", updater.Name);
+                applied.Add(updater.Name);
+            }
+
+            if (applied.Count > migrationOptions.Applied.Length)
+            {
+                logger.LogInformation("Some migrations were run, saving the state");
+                migrationOptions.Applied = applied.ToArray();
+                host.ServerConfigurationManager.SaveConfiguration(MigrationsListStore.StoreKey, migrationOptions);
+            }
+        }
+    }
+}
diff --git a/Jellyfin.Server/Migrations/MigrationsFactory.cs b/Jellyfin.Server/Migrations/MigrationsFactory.cs
new file mode 100644
index 0000000000..23c1b1ee6f
--- /dev/null
+++ b/Jellyfin.Server/Migrations/MigrationsFactory.cs
@@ -0,0 +1,20 @@
+using System.Collections.Generic;
+using MediaBrowser.Common.Configuration;
+
+namespace Jellyfin.Server.Migrations
+{
+    /// <summary>
+    /// A factory that can find a persistent file of the migration configuration, which lists all applied migrations.
+    /// </summary>
+    public class MigrationsFactory : IConfigurationFactory
+    {
+        /// <inheritdoc/>
+        public IEnumerable<ConfigurationStore> GetConfigurations()
+        {
+            return new[]
+            {
+                new MigrationsListStore()
+            };
+        }
+    }
+}
diff --git a/Jellyfin.Server/Migrations/MigrationsListStore.cs b/Jellyfin.Server/Migrations/MigrationsListStore.cs
new file mode 100644
index 0000000000..7a1ca66714
--- /dev/null
+++ b/Jellyfin.Server/Migrations/MigrationsListStore.cs
@@ -0,0 +1,24 @@
+using MediaBrowser.Common.Configuration;
+
+namespace Jellyfin.Server.Migrations
+{
+    /// <summary>
+    /// A configuration that lists all the migration routines that were applied.
+    /// </summary>
+    public class MigrationsListStore : ConfigurationStore
+    {
+        /// <summary>
+        /// The name of the configuration in the storage.
+        /// </summary>
+        public static readonly string StoreKey = "migrations";
+
+        /// <summary>
+        /// Initializes a new instance of the <see cref="MigrationsListStore"/> class.
+        /// </summary>
+        public MigrationsListStore()
+        {
+            ConfigurationType = typeof(MigrationOptions);
+            Key = StoreKey;
+        }
+    }
+}
diff --git a/Jellyfin.Server/Migrations/Routines/DisableTranscodingThrottling.cs b/Jellyfin.Server/Migrations/Routines/DisableTranscodingThrottling.cs
new file mode 100644
index 0000000000..936c3640e0
--- /dev/null
+++ b/Jellyfin.Server/Migrations/Routines/DisableTranscodingThrottling.cs
@@ -0,0 +1,32 @@
+using System;
+using System.IO;
+using MediaBrowser.Common.Configuration;
+using MediaBrowser.Model.Configuration;
+using Microsoft.Extensions.Configuration;
+using Microsoft.Extensions.Logging;
+
+namespace Jellyfin.Server.Migrations.Routines
+{
+    /// <summary>
+    /// Disable transcode throttling for all installations since it is currently broken for certain video formats.
+    /// </summary>
+    internal class DisableTranscodingThrottling : IUpdater
+    {
+        /// <inheritdoc/>
+        public string Name => "DisableTranscodingThrottling";
+
+        /// <inheritdoc/>
+        public void Perform(CoreAppHost host, ILogger logger)
+        {
+            // Set EnableThrottling to false since it wasn't used before and may introduce issues
+            var encoding = ((IConfigurationManager)host.ServerConfigurationManager).GetConfiguration<EncodingOptions>("encoding");
+            if (encoding.EnableThrottling)
+            {
+                logger.LogInformation("Disabling transcoding throttling during migration");
+                encoding.EnableThrottling = false;
+
+                host.ServerConfigurationManager.SaveConfiguration("encoding", encoding);
+            }
+        }
+    }
+}
diff --git a/Jellyfin.Server/Migrations/Routines/DisableZealousLogging.cs b/Jellyfin.Server/Migrations/Routines/DisableZealousLogging.cs
new file mode 100644
index 0000000000..501f8f8654
--- /dev/null
+++ b/Jellyfin.Server/Migrations/Routines/DisableZealousLogging.cs
@@ -0,0 +1,29 @@
+using System;
+using System.IO;
+using MediaBrowser.Common.Configuration;
+using MediaBrowser.Model.Configuration;
+using Microsoft.Extensions.Configuration;
+using Microsoft.Extensions.Logging;
+using Serilog;
+using ILogger = Microsoft.Extensions.Logging.ILogger;
+
+namespace Jellyfin.Server.Migrations.Routines
+{
+    /// <summary>
+    /// Updater that takes care of bringing configuration up to 10.5.0 standards.
+    /// </summary>
+    internal class DisableZealousLogging : IUpdater
+    {
+        /// <inheritdoc/>
+        public string Name => "DisableZealousLogging";
+
+        /// <inheritdoc/>
+        // This tones down logging from some components
+        public void Perform(CoreAppHost host, ILogger logger)
+        {
+            string configPath = Path.Combine(host.ServerConfigurationManager.ApplicationPaths.ConfigurationDirectoryPath, Program.LoggingConfigFile);
+            // TODO: fix up the config
+            throw new NotImplementedException("don't know how to fix logging yet");
+        }
+    }
+}
diff --git a/Jellyfin.Server/Program.cs b/Jellyfin.Server/Program.cs
index aa1bdb1691..0271861054 100644
--- a/Jellyfin.Server/Program.cs
+++ b/Jellyfin.Server/Program.cs
@@ -38,6 +38,11 @@ namespace Jellyfin.Server
     /// </summary>
     public static class Program
     {
+        /// <summary>
+        /// The name of logging configuration file.
+        /// </summary>
+        public static readonly string LoggingConfigFile = "logging.json";
+
         private static readonly CancellationTokenSource _tokenSource = new CancellationTokenSource();
         private static readonly ILoggerFactory _loggerFactory = new SerilogLoggerFactory();
         private static ILogger _logger = NullLogger.Instance;
@@ -182,7 +187,7 @@ namespace Jellyfin.Server
                 // A bit hacky to re-use service provider since ASP.NET doesn't allow a custom service collection.
                 appHost.ServiceProvider = host.Services;
                 appHost.FindParts();
-                appHost.TryMigrate();
+                Migrations.MigrationRunner.Run(appHost, _loggerFactory);
 
                 try
                 {
@@ -438,7 +443,7 @@ namespace Jellyfin.Server
         private static async Task<IConfiguration> CreateConfiguration(IApplicationPaths appPaths)
         {
             const string ResourcePath = "Jellyfin.Server.Resources.Configuration.logging.json";
-            string configPath = Path.Combine(appPaths.ConfigurationDirectoryPath, "logging.json");
+            string configPath = Path.Combine(appPaths.ConfigurationDirectoryPath, LoggingConfigFile);
 
             if (!File.Exists(configPath))
             {
@@ -460,7 +465,7 @@ namespace Jellyfin.Server
             return new ConfigurationBuilder()
                 .SetBasePath(appPaths.ConfigurationDirectoryPath)
                 .AddInMemoryCollection(ConfigurationOptions.Configuration)
-                .AddJsonFile("logging.json", false, true)
+                .AddJsonFile(LoggingConfigFile, false, true)
                 .AddEnvironmentVariables("JELLYFIN_")
                 .Build();
         }