diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/backup/BackupRestoreService.kt b/app/src/main/java/eu/kanade/tachiyomi/data/backup/BackupRestoreService.kt
index c82e4f2ee9..873484ff91 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/backup/BackupRestoreService.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/backup/BackupRestoreService.kt
@@ -43,6 +43,7 @@ import uy.kohesive.injekt.injectLazy
 import java.io.File
 import java.text.SimpleDateFormat
 import java.util.Locale
+import java.util.concurrent.TimeUnit
 
 /**
  * Restores backup from json file
@@ -117,7 +118,7 @@ class BackupRestoreService : Service() {
         startForeground(Notifications.ID_RESTORE_PROGRESS, progressNotification.build())
         wakeLock = (getSystemService(Context.POWER_SERVICE) as PowerManager).newWakeLock(
                 PowerManager.PARTIAL_WAKE_LOCK, "BackupRestoreService:WakeLock")
-        wakeLock.acquire()
+        wakeLock.acquire(TimeUnit.HOURS.toMillis(3))
     }
 
     /**
diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt
index 9061a997ef..c54d8db8f9 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadCache.kt
@@ -217,6 +217,17 @@ class DownloadCache(
         }
     }
 
+    fun removeFolders(folders: List<String>, manga: Manga) {
+        val sourceDir = rootDir.files[manga.source] ?: return
+        val mangaDir = sourceDir.files[provider.getMangaDirName(manga)] ?: return
+        for (chapter in folders) {
+            if (chapter in mangaDir.files) {
+                mangaDir.files -= chapter
+            }
+        }
+    }
+
+
     /**
      * Removes a manga that has been deleted from this cache.
      *
diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadManager.kt b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadManager.kt
index f2470be65a..4e6622ea21 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadManager.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadManager.kt
@@ -219,16 +219,21 @@ class DownloadManager(val context: Context) {
      * @param manga the manga of the chapters.
      * @param source the source of the chapters.
      */
-    fun cleanupChapters(allChapters: List<Chapter>, manga: Manga, source: Source) {
+    fun cleanupChapters(allChapters: List<Chapter>, manga: Manga, source: Source): Int {
+        var cleaned = 0
         val filesWithNoChapter = provider.findUnmatchedChapterDirs(allChapters, manga, source)
+        cleaned += filesWithNoChapter.size
+        cache.removeFolders(filesWithNoChapter.mapNotNull { it.name }, manga)
         filesWithNoChapter.forEach { it.delete() }
         val readChapters = allChapters.filter { it.read }
         val readChapterDirs = provider.findChapterDirs(readChapters, manga, source)
         readChapterDirs.forEach { it.delete() }
+        cleaned += readChapterDirs.size
         cache.removeChapters(readChapters, manga)
         if (cache.getDownloadCount(manga) == 0) {
             provider.findChapterDirs(allChapters, manga, source).firstOrNull()?.parentFile?.delete()// Delete manga directory if empty
         }
+        return cleaned
     }
 
     /**
diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadProvider.kt b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadProvider.kt
index 2cce3e479d..c12aa1c639 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadProvider.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/download/DownloadProvider.kt
@@ -142,13 +142,11 @@ class DownloadProvider(private val context: Context) {
     fun findUnmatchedChapterDirs(chapters: List<Chapter>, manga: Manga, source: Source): List<UniFile> {
         val mangaDir = findMangaDir(manga, source) ?: return emptyList()
         return mangaDir.listFiles()!!.asList().filter {
-            chapters.find { chp ->
-                (getValidChapterDirNames(chp) + "${getChapterDirName(chp)}_tmp").any { dir ->
-                    mangaDir.findFile(
-                        dir
-                    ) != null
+            (chapters.find { chp ->
+                getValidChapterDirNames(chp).any { dir ->
+                    mangaDir.findFile(dir) != null
                 }
-            } == null
+            } == null) || it.name?.endsWith("_tmp") == true
         }
     }
 
diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/library/LibraryUpdateService.kt b/app/src/main/java/eu/kanade/tachiyomi/data/library/LibraryUpdateService.kt
index 8b9c8e635b..9029ea5510 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/library/LibraryUpdateService.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/library/LibraryUpdateService.kt
@@ -40,9 +40,6 @@ import eu.kanade.tachiyomi.util.notification
 import eu.kanade.tachiyomi.util.notificationManager
 import eu.kanade.tachiyomi.util.syncChaptersWithSource
 import kotlinx.coroutines.CoroutineExceptionHandler
-import kotlinx.coroutines.GlobalScope
-import kotlinx.coroutines.Job
-import kotlinx.coroutines.launch
 import rx.Observable
 import rx.Subscription
 import rx.schedulers.Schedulers
@@ -52,6 +49,7 @@ import uy.kohesive.injekt.api.get
 import uy.kohesive.injekt.injectLazy
 import java.util.ArrayList
 import java.util.Date
+import java.util.concurrent.TimeUnit
 import java.util.concurrent.atomic.AtomicInteger
 
 /**
@@ -80,8 +78,6 @@ class LibraryUpdateService(
      */
     private var subscription: Subscription? = null
 
-    var job: Job? = null
-
 
     /**
      * Pending intent of action that cancels the library update
@@ -116,8 +112,7 @@ class LibraryUpdateService(
     enum class Target {
         CHAPTERS, // Manga chapters
         DETAILS,  // Manga metadata
-        TRACKING,  // Tracking metadata
-        CLEANUP // Clean up downloads
+        TRACKING  // Tracking metadata
     }
 
     companion object {
@@ -184,7 +179,7 @@ class LibraryUpdateService(
         startForeground(Notifications.ID_LIBRARY_PROGRESS, progressNotification.build())
         wakeLock = (getSystemService(Context.POWER_SERVICE) as PowerManager).newWakeLock(
                 PowerManager.PARTIAL_WAKE_LOCK, "LibraryUpdateService:WakeLock")
-        wakeLock.acquire()
+        wakeLock.acquire(TimeUnit.MINUTES.toMillis(30))
     }
 
     /**
@@ -222,22 +217,16 @@ class LibraryUpdateService(
         // Unsubscribe from any previous subscription if needed.
         subscription?.unsubscribe()
 
-        val selectedScheme = preferences.libraryUpdatePrioritization().getOrDefault()
-        // Update favorite manga. Destroy service when completed or in case of an error.
-        val mangaList = getMangaToUpdate(intent, target)
-                .sortedWith(rankingScheme[selectedScheme])
 
         val handler = CoroutineExceptionHandler { _, exception ->
             Timber.e(exception)
             stopSelf(startId)
         }
         // Update either chapter list or manga details.
-        if (target == Target.CLEANUP) {
-            job = GlobalScope.launch(handler) {
-                cleanupDownloads()
-            }
-            job?.invokeOnCompletion { stopSelf(startId) }
-        } else {
+        val selectedScheme = preferences.libraryUpdatePrioritization().getOrDefault()
+            // Update favorite manga. Destroy service when completed or in case of an error.
+            val mangaList = getMangaToUpdate(intent, target)
+                .sortedWith(rankingScheme[selectedScheme])
             subscription = Observable.defer {
                 when (target) {
                     Target.CHAPTERS -> updateChapterList(mangaList)
@@ -250,7 +239,6 @@ class LibraryUpdateService(
                 }, {
                     stopSelf(startId)
                 })
-        }
         return START_REDELIVER_INTENT
     }
 
@@ -360,11 +348,13 @@ class LibraryUpdateService(
 
     private fun cleanupDownloads() {
         val mangaList = db.getMangas().executeAsBlocking()
+        var foldersCleared = 0
         for (manga in mangaList) {
             val chapterList = db.getChapters(manga).executeAsBlocking()
             val source = sourceManager.getOrStub(manga.source)
-            downloadManager.cleanupChapters(chapterList, manga, source)
+            foldersCleared += downloadManager.cleanupChapters(chapterList, manga, source)
         }
+
     }
 
     fun downloadChapters(manga: Manga, chapters: List<Chapter>) {
diff --git a/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsAdvancedController.kt b/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsAdvancedController.kt
index 0e48f2edce..421693fff6 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsAdvancedController.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsAdvancedController.kt
@@ -4,21 +4,33 @@ import android.app.Dialog
 import android.os.Bundle
 import androidx.preference.PreferenceScreen
 import android.view.View
+import android.widget.Toast
 import com.afollestad.materialdialogs.MaterialDialog
 import com.bluelinelabs.conductor.RouterTransaction
 import com.bluelinelabs.conductor.changehandler.FadeChangeHandler
 import eu.kanade.tachiyomi.R
 import eu.kanade.tachiyomi.data.cache.ChapterCache
 import eu.kanade.tachiyomi.data.database.DatabaseHelper
+import eu.kanade.tachiyomi.data.download.DownloadManager
 import eu.kanade.tachiyomi.data.library.LibraryUpdateService
 import eu.kanade.tachiyomi.data.library.LibraryUpdateService.Target
+import eu.kanade.tachiyomi.data.preference.PreferencesHelper
 import eu.kanade.tachiyomi.network.NetworkHelper
+import eu.kanade.tachiyomi.source.SourceManager
 import eu.kanade.tachiyomi.ui.base.controller.DialogController
 import eu.kanade.tachiyomi.ui.library.LibraryController
+import eu.kanade.tachiyomi.util.launchUI
 import eu.kanade.tachiyomi.util.toast
+import kotlinx.coroutines.CoroutineStart
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.GlobalScope
+import kotlinx.coroutines.Job
+import kotlinx.coroutines.launch
 import rx.Observable
 import rx.android.schedulers.AndroidSchedulers
 import rx.schedulers.Schedulers
+import uy.kohesive.injekt.Injekt
+import uy.kohesive.injekt.api.get
 import uy.kohesive.injekt.injectLazy
 
 class SettingsAdvancedController : SettingsController() {
@@ -74,10 +86,33 @@ class SettingsAdvancedController : SettingsController() {
 
             summaryRes = R.string.pref_clean_downloads_summary
 
-            onClick { LibraryUpdateService.start(context, target = Target.CLEANUP) }
+            onClick { cleanupDownloads() }
         }
     }
 
+    private fun cleanupDownloads() {
+        if (job?.isActive == true) return
+        activity?.toast(R.string.starting_cleanup)
+        job = GlobalScope.launch(Dispatchers.IO, CoroutineStart.DEFAULT) {
+            val mangaList = db.getMangas().executeAsBlocking()
+            val sourceManager: SourceManager = Injekt.get()
+            val downloadManager: DownloadManager = Injekt.get()
+            var foldersCleared = 0
+            for (manga in mangaList) {
+                val chapterList = db.getChapters(manga).executeAsBlocking()
+                val source = sourceManager.getOrStub(manga.source)
+                foldersCleared += downloadManager.cleanupChapters(chapterList, manga, source)
+            }
+            launchUI {
+                val activity = activity ?: return@launchUI
+                val cleanupString = if (foldersCleared == 0) activity.getString(R.string.no_cleanup_done)
+                else resources!!.getQuantityString(R.plurals.cleanup_done, foldersCleared, foldersCleared)
+                activity.toast(cleanupString, Toast.LENGTH_LONG)
+            }
+        }
+
+    }
+
     private fun clearChapterCache() {
         if (activity == null) return
         val files = chapterCache.cacheDir.listFiles() ?: return
@@ -128,5 +163,7 @@ class SettingsAdvancedController : SettingsController() {
 
     private companion object {
         const val CLEAR_CACHE_KEY = "pref_clear_cache_key"
+
+        private var job: Job? = null
     }
 }
diff --git a/app/src/main/res/values/strings.xml b/app/src/main/res/values/strings.xml
index 3e32aba0c8..6376cf9897 100644
--- a/app/src/main/res/values/strings.xml
+++ b/app/src/main/res/values/strings.xml
@@ -355,9 +355,16 @@
     <string name="pref_refresh_library_tracking">Refresh tracking metadata</string>
     <string name="pref_refresh_library_tracking_summary">Updates status, score and last chapter read from the tracking services</string>
     <string name="pref_clean_downloads">Clean up downloaded chapters</string>
-        <string name="pref_clean_downloads_summary">Deletes non-existent, partially downloaded,
+    <string name="pref_clean_downloads_summary">Delete non-existent, partially downloaded,
             and read chapter folders</string>
 
+    <string name="starting_cleanup">Starting cleanup</string>
+    <string name="no_cleanup_done">No folders to cleanup</string>
+    <plurals name="cleanup_done">
+        <item quantity="one">Cleanup done. Removed %d folder</item>
+        <item quantity="other">Cleanup done. Removed %d folders</item>
+    </plurals>
+
       <!-- About section -->
     <string name="version">Version</string>
     <string name="build_time">Build time</string>