diff --git a/server/src/main/kotlin/suwayomi/tachidesk/server/Migration.kt b/server/src/main/kotlin/suwayomi/tachidesk/server/Migration.kt
new file mode 100644
index 000000000..381b504ae
--- /dev/null
+++ b/server/src/main/kotlin/suwayomi/tachidesk/server/Migration.kt
@@ -0,0 +1,86 @@
+package suwayomi.tachidesk.server
+
+import android.app.Application
+import android.content.Context
+import mu.KotlinLogging
+import uy.kohesive.injekt.Injekt
+import uy.kohesive.injekt.api.get
+import java.io.File
+import java.util.prefs.Preferences
+
+private fun migratePreferences(
+    parent: String?,
+    rootNode: Preferences,
+) {
+    val subNodes = rootNode.childrenNames()
+
+    for (subNodeName in subNodes) {
+        val subNode = rootNode.node(subNodeName)
+        val key =
+            if (parent != null) {
+                "$parent/$subNodeName"
+            } else {
+                subNodeName
+            }
+        val preferences = Injekt.get<Application>().getSharedPreferences(key, Context.MODE_PRIVATE)
+
+        val items: Map<String, String?> =
+            subNode.keys().associateWith {
+                subNode[it, null]?.ifBlank { null }
+            }
+
+        preferences.edit().apply {
+            items.forEach { (key, value) ->
+                if (value != null) {
+                    putString(key, value)
+                }
+            }
+        }.apply()
+
+        migratePreferences(key, subNode) // Recursively migrate sub-level nodes
+    }
+}
+
+const val MIGRATION_VERSION = 1
+
+fun runMigrations(applicationDirs: ApplicationDirs) {
+    val migrationPreferences =
+        Injekt.get<Application>()
+            .getSharedPreferences(
+                "migrations",
+                Context.MODE_PRIVATE,
+            )
+    val version = migrationPreferences.getInt("version", 0)
+    val logger = KotlinLogging.logger("Migration")
+    logger.info { "Running migrations, previous version $version, target version $MIGRATION_VERSION" }
+
+    if (version < 1) {
+        logger.info { "Running migration for version: 1" }
+        val oldMangaDownloadDir = File(applicationDirs.downloadsRoot)
+        val newMangaDownloadDir = File(applicationDirs.mangaDownloadsRoot)
+        val downloadDirs = oldMangaDownloadDir.listFiles().orEmpty()
+
+        val moveDownloadsToNewFolder = !newMangaDownloadDir.exists() && downloadDirs.isNotEmpty()
+        if (moveDownloadsToNewFolder) {
+            newMangaDownloadDir.mkdirs()
+
+            for (downloadDir in downloadDirs) {
+                if (downloadDir == File(applicationDirs.thumbnailDownloadsRoot)) {
+                    continue
+                }
+
+                downloadDir.renameTo(File(newMangaDownloadDir, downloadDir.name))
+            }
+        }
+
+        // Migrate from old preferences api
+        val prefRootNode = "suwayomi/tachidesk"
+        val isMigrationRequired = Preferences.userRoot().nodeExists(prefRootNode)
+        if (isMigrationRequired) {
+            val preferences = Preferences.userRoot().node(prefRootNode)
+            migratePreferences(null, preferences)
+            preferences.removeNode()
+        }
+    }
+    migrationPreferences.edit().putInt("version", MIGRATION_VERSION).apply()
+}
diff --git a/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt b/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt
index f1b9cbc65..864c2a3f3 100644
--- a/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt
+++ b/server/src/main/kotlin/suwayomi/tachidesk/server/ServerSetup.kt
@@ -7,8 +7,6 @@ package suwayomi.tachidesk.server
  * License, v. 2.0. If a copy of the MPL was not distributed with this
  * file, You can obtain one at https://mozilla.org/MPL/2.0/. */
 
-import android.app.Application
-import android.content.Context
 import ch.qos.logback.classic.Level
 import com.typesafe.config.ConfigRenderOptions
 import eu.kanade.tachiyomi.App
@@ -34,7 +32,6 @@ import suwayomi.tachidesk.server.database.databaseUp
 import suwayomi.tachidesk.server.generated.BuildConfig
 import suwayomi.tachidesk.server.util.AppMutex.handleAppMutex
 import suwayomi.tachidesk.server.util.SystemTray
-import uy.kohesive.injekt.Injekt
 import uy.kohesive.injekt.api.get
 import xyz.nulldev.androidcompat.AndroidCompat
 import xyz.nulldev.androidcompat.AndroidCompatInitializer
@@ -47,7 +44,6 @@ import xyz.nulldev.ts.config.setLogLevelFor
 import java.io.File
 import java.security.Security
 import java.util.Locale
-import java.util.prefs.Preferences
 
 private val logger = KotlinLogging.logger {}
 
@@ -126,23 +122,6 @@ fun applicationSetup() {
     File("$ApplicationRootDir/manga-local").renameTo(applicationDirs.localMangaRoot)
     File("$ApplicationRootDir/anime-thumbnails").delete()
 
-    val oldMangaDownloadDir = File(applicationDirs.downloadsRoot)
-    val newMangaDownloadDir = File(applicationDirs.mangaDownloadsRoot)
-    val downloadDirs = oldMangaDownloadDir.listFiles().orEmpty()
-
-    val moveDownloadsToNewFolder = !newMangaDownloadDir.exists() && downloadDirs.isNotEmpty()
-    if (moveDownloadsToNewFolder) {
-        newMangaDownloadDir.mkdirs()
-
-        for (downloadDir in downloadDirs) {
-            if (downloadDir == File(applicationDirs.thumbnailDownloadsRoot)) {
-                continue
-            }
-
-            downloadDir.renameTo(File(newMangaDownloadDir, downloadDir.name))
-        }
-    }
-
     // make dirs we need
     listOf(
         applicationDirs.dataRoot,
@@ -217,13 +196,7 @@ fun applicationSetup() {
         }
     }, ignoreInitialValue = false)
 
-    val prefRootNode = "suwayomi/tachidesk"
-    val isMigrationRequired = Preferences.userRoot().nodeExists(prefRootNode)
-    if (isMigrationRequired) {
-        val preferences = Preferences.userRoot().node(prefRootNode)
-        migratePreferences(null, preferences)
-        preferences.removeNode()
-    }
+    runMigrations(applicationDirs)
 
     // Disable jetty's logging
     System.setProperty("org.eclipse.jetty.util.log.announce", "false")
@@ -265,36 +238,3 @@ fun applicationSetup() {
     // start DownloadManager and restore + resume downloads
     DownloadManager.restoreAndResumeDownloads()
 }
-
-fun migratePreferences(
-    parent: String?,
-    rootNode: Preferences,
-) {
-    val subNodes = rootNode.childrenNames()
-
-    for (subNodeName in subNodes) {
-        val subNode = rootNode.node(subNodeName)
-        val key =
-            if (parent != null) {
-                "$parent/$subNodeName"
-            } else {
-                subNodeName
-            }
-        val preferences = Injekt.get<Application>().getSharedPreferences(key, Context.MODE_PRIVATE)
-
-        val items: Map<String, String?> =
-            subNode.keys().associateWith {
-                subNode[it, null]?.ifBlank { null }
-            }
-
-        preferences.edit().apply {
-            items.forEach { (key, value) ->
-                if (value != null) {
-                    putString(key, value)
-                }
-            }
-        }.apply()
-
-        migratePreferences(key, subNode) // Recursively migrate sub-level nodes
-    }
-}