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 60190eb126..b46ba1f262 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
@@ -105,6 +105,11 @@ class LibraryUpdateService(
     // List containing new updates
     private val newUpdates = mutableMapOf<LibraryManga, Array<Chapter>>()
 
+    // For updates delete removed chapters if not preference is set as well
+    private val deleteRemoved by lazy {
+        preferences.deleteRemovedChapters().get() != 1
+    }
+
     /**
      * Cached progress notification to avoid creating a lot.
      */
@@ -415,6 +420,14 @@ class LibraryUpdateService(
                     newUpdates[manga] =
                         newChapters.first.sortedBy { it.chapter_number }.toTypedArray()
                 }
+                if (deleteRemoved && newChapters.second.isNotEmpty()) {
+                    val removedChapters = newChapters.second.filter {
+                        downloadManager.isChapterDownloaded(it, manga)
+                    }
+                    if (removedChapters.isNotEmpty()) {
+                        downloadManager.deleteChapters(removedChapters, manga, source)
+                    }
+                }
                 if (newChapters.first.size + newChapters.second.size > 0) listener?.onUpdateManga(
                     manga
                 )
diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferenceKeys.kt b/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferenceKeys.kt
index c510b9c110..c4714e2ab8 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferenceKeys.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferenceKeys.kt
@@ -79,6 +79,8 @@ object PreferenceKeys {
 
     const val removeAfterReadSlots = "remove_after_read_slots"
 
+    const val deleteRemovedChapters = "delete_removed_chapters"
+
     const val removeAfterMarkedAsRead = "pref_remove_after_marked_as_read_key"
 
     const val libraryUpdateInterval = "pref_library_update_interval_key"
diff --git a/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferencesHelper.kt b/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferencesHelper.kt
index 09e32a31c6..19a47e1b5b 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferencesHelper.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/data/preference/PreferencesHelper.kt
@@ -261,7 +261,9 @@ class PreferencesHelper(val context: Context) {
 
     fun alwaysShowChapterTransition() = rxPrefs.getBoolean(Keys.alwaysShowChapterTransition, true)
 
-    // Tutorial preference
+    fun deleteRemovedChapters() = flowPrefs.getInt(Keys.deleteRemovedChapters, 0)
+
+    // Tutorial preferences
     fun shownFilterTutorial() = flowPrefs.getBoolean("shown_filter_tutorial", false)
 
     fun shownChapterSwipeTutorial() = flowPrefs.getBoolean("shown_swipe_tutorial", false)
diff --git a/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsController.kt b/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsController.kt
index b1e7959f67..abe99d2cb3 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsController.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsController.kt
@@ -45,6 +45,8 @@ import androidx.transition.ChangeImageTransform
 import androidx.transition.TransitionManager
 import androidx.transition.TransitionSet
 import com.afollestad.materialdialogs.MaterialDialog
+import com.afollestad.materialdialogs.checkbox.checkBoxPrompt
+import com.afollestad.materialdialogs.checkbox.isCheckPromptChecked
 import com.afollestad.materialdialogs.list.listItems
 import com.bluelinelabs.conductor.ControllerChangeHandler
 import com.bluelinelabs.conductor.ControllerChangeType
@@ -575,6 +577,31 @@ class MangaDetailsController : BaseController,
         view?.snack(message)
     }
 
+    fun showChaptersRemovedPopup(deletedChapters: List<ChapterItem>) {
+        val context = activity ?: return
+        val deleteRemovedPref = presenter.preferences.deleteRemovedChapters()
+        when (deleteRemovedPref.get()) {
+            2 -> {
+                presenter.deleteChapters(deletedChapters, false)
+                return
+            }
+            1 -> return
+            else -> {
+                MaterialDialog(context).title(R.string.chapters_removed).message(
+                    text = context.resources.getQuantityString(R.plurals.deleted_chapters,
+                        deletedChapters.size,
+                        deletedChapters.size,
+                        deletedChapters.joinToString("\n") { "${it.name}" })
+                ).positiveButton(R.string.delete) {
+                    presenter.deleteChapters(deletedChapters, false)
+                    if (it.isCheckPromptChecked()) deleteRemovedPref.set(2)
+                }.negativeButton(R.string.keep) {
+                    if (it.isCheckPromptChecked()) deleteRemovedPref.set(1)
+                }.cancelOnTouchOutside(false).checkBoxPrompt(R.string.remember_this_choice) {}.show()
+            }
+        }
+    }
+
     fun setRefresh(enabled: Boolean) {
         swipe_refresh.isRefreshing = enabled
     }
diff --git a/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsPresenter.kt b/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsPresenter.kt
index 9d11131868..8820b2d55e 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsPresenter.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/ui/manga/MangaDetailsPresenter.kt
@@ -423,6 +423,19 @@ class MangaDetailsPresenter(
                             .map { it.toModel() })
                     }
                 }
+                if (newChapters.second.isNotEmpty()) {
+                    val removedChaptersId = newChapters.second.map { it.id }
+                    val removedChapters = this@MangaDetailsPresenter.chapters.filter {
+                        it.id in removedChaptersId && it.isDownloaded
+                    }
+                    if (removedChapters.isNotEmpty()) {
+                        withContext(Dispatchers.Main) {
+                            controller.showChaptersRemovedPopup(
+                                removedChapters
+                            )
+                        }
+                    }
+                }
                 withContext(Dispatchers.IO) { updateChapters() }
             }
             isLoading = false
diff --git a/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsDownloadController.kt b/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsDownloadController.kt
index f282d2f15a..995352527e 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsDownloadController.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/ui/setting/SettingsDownloadController.kt
@@ -102,6 +102,20 @@ class SettingsDownloadController : SettingsController() {
                                 selectedCategories.joinToString { it.name }
                         }
             }
+            preferenceCategory {
+                intListPreference(activity) {
+                    key = Keys.deleteRemovedChapters
+                    titleRes = R.string.delete_removed_chapters
+                    customSummary = activity?.getString(R.string.delete_downloaded_if_removed_online)
+                    entriesRes = arrayOf(
+                        R.string.ask_on_chapters_page,
+                        R.string.always_keep,
+                        R.string.always_delete
+                    )
+                    entryRange = 0..2
+                    defaultValue = 0
+                }
+            }
         }
     }
 
diff --git a/app/src/main/java/eu/kanade/tachiyomi/util/chapter/ChapterSourceSync.kt b/app/src/main/java/eu/kanade/tachiyomi/util/chapter/ChapterSourceSync.kt
index 4776dd7fff..85394c5d15 100644
--- a/app/src/main/java/eu/kanade/tachiyomi/util/chapter/ChapterSourceSync.kt
+++ b/app/src/main/java/eu/kanade/tachiyomi/util/chapter/ChapterSourceSync.kt
@@ -149,7 +149,7 @@ fun syncChaptersWithSource(
         db.updateLastUpdated(manga).executeAsBlocking()
     }
 
-    return Pair(toAdd.subtract(readded).toList(), toDelete.subtract(readded).toList())
+    return Pair(toAdd.subtract(readded).toList(), toDelete - readded)
 }
 
 // checks if the chapter in db needs updated
diff --git a/app/src/main/res/values/strings.xml b/app/src/main/res/values/strings.xml
index 26b6b3935d..95938eae2e 100644
--- a/app/src/main/res/values/strings.xml
+++ b/app/src/main/res/values/strings.xml
@@ -47,6 +47,7 @@
     <string name="marked_as_read">Marked as read</string>
     <string name="marked_as_unread">Marked as unread</string>
     <string name="removed_bookmark">Removed bookmark</string>
+    <string name="chapters_removed">Chapters removed.</string>
     <plurals name="remove_n_chapters">
         <item quantity="one">Remove %1$d downloaded chapter?</item>
         <item quantity="other">Remove %1$d downloaded chapters?</item>
@@ -368,6 +369,13 @@
     <string name="reset_cover">Reset cover</string>
     <string name="failed_to_update_cover">Failed to update cover</string>
     <string name="must_be_in_library_to_edit">Manga must be in your library to edit</string>
+    <string name="remember_this_choice">Remember this choice</string>
+    <plurals name="deleted_chapters">
+        <item quantity="one">A chapter has been removed from the source:\n%2$s\nDelete
+            its download?</item>
+        <item quantity="other">%1$s chapters have been removed from the source:\n%2$s\n\nDelete
+            their downloads?</item>
+    </plurals>
 
     <!-- Tracking -->
     <string name="tracking">Tracking</string>
@@ -575,6 +583,12 @@
     <string name="fifth_to_last">Fifth to last chapter</string>
     <string name="download_new_chapters">Download new chapters</string>
     <string name="categories_to_include_in_download">Categories to include in download</string>
+    <string name="delete_removed_chapters">Delete removed chapters</string>
+    <string name="delete_downloaded_if_removed_online">Delete downloaded chapters if the source
+        has removed the chapter online</string>
+    <string name="ask_on_chapters_page">Delete during global updates, ask on chapters page</string>
+    <string name="always_keep">Always keep</string>
+    <string name="always_delete">Always delete</string>
 
     <!-- Time -->
     <string name="manual">Manual</string>
@@ -633,6 +647,7 @@
     <string name="hide">Hide</string>
     <string name="ignore">Ignore</string>
     <string name="install">Install</string>
+    <string name="keep">Keep</string>
     <string name="left">Left</string>
     <string name="less">Less</string>
     <string name="loading">Loading…</string>