diff --git a/src/calibre/ebooks/oeb/polish/main.py b/src/calibre/ebooks/oeb/polish/main.py
index 51b7db77ac..509a9c761a 100644
--- a/src/calibre/ebooks/oeb/polish/main.py
+++ b/src/calibre/ebooks/oeb/polish/main.py
@@ -44,6 +44,7 @@ CUSTOMIZATION = {
     'remove_unused_classes': False,
     'merge_identical_selectors': False,
     'merge_rules_with_identical_properties': False,
+    'remove_ncx': True,
 }
 
 SUPPORTED = {'EPUB', 'AZW3'}
@@ -250,7 +251,7 @@ def polish_one(ebook, opts, report, customization=None):
 
     if opts.upgrade_book:
         rt(_('Upgrading book, if possible'))
-        if upgrade_book(ebook, report):
+        if upgrade_book(ebook, report, remove_ncx=customization['remove_ncx']):
             changed = True
         report('')
 
diff --git a/src/calibre/ebooks/oeb/polish/upgrade.py b/src/calibre/ebooks/oeb/polish/upgrade.py
index e98a8d8471..44a01429bc 100644
--- a/src/calibre/ebooks/oeb/polish/upgrade.py
+++ b/src/calibre/ebooks/oeb/polish/upgrade.py
@@ -114,12 +114,12 @@ def create_nav(container, toc, landmarks, previous_nav=None):
     commit_nav_toc(container, toc, lang=lang, landmarks=landmarks, previous_nav=previous_nav)
 
 
-def epub_2_to_3(container, report, previous_nav=None):
+def epub_2_to_3(container, report, previous_nav=None, remove_ncx=True):
     upgrade_metadata(container.opf)
     collect_properties(container)
     toc = get_toc(container)
     toc_name = find_existing_ncx_toc(container)
-    if toc_name:
+    if toc_name and remove_ncx:
         container.remove_item(toc_name)
     container.opf_xpath('./opf:spine')[0].attrib.pop('toc', None)
     landmarks = get_landmarks(container)
@@ -132,11 +132,11 @@ def epub_2_to_3(container, report, previous_nav=None):
     container.dirty(container.opf_name)
 
 
-def upgrade_book(container, report):
+def upgrade_book(container, report, remove_ncx=True):
     if container.book_type != 'epub' or container.opf_version_parsed.major >= 3:
         report(_('No upgrade needed'))
         return False
-    epub_2_to_3(container, report)
+    epub_2_to_3(container, report, remove_ncx=remove_ncx)
     report(_('Updated EPUB from version 2 to 3'))
     return True
 
diff --git a/src/calibre/gui2/tweak_book/polish.py b/src/calibre/gui2/tweak_book/polish.py
index c9d41b9621..fd148c698f 100644
--- a/src/calibre/gui2/tweak_book/polish.py
+++ b/src/calibre/gui2/tweak_book/polish.py
@@ -17,7 +17,7 @@ from PyQt5.Qt import (
 
 from calibre import human_readable, fit_image, force_unicode
 from calibre.ebooks.oeb.polish.main import CUSTOMIZATION
-from calibre.gui2 import empty_index
+from calibre.gui2 import empty_index, question_dialog
 from calibre.gui2.tweak_book import tprefs, current_container, set_current_container
 from calibre.gui2.tweak_book.widgets import Dialog
 from calibre.utils.icu import numeric_sort_key
@@ -78,6 +78,17 @@ def get_customization(action, name, parent):
     try:
         if action == 'remove_unused_css':
             customize_remove_unused_css(name, parent, ans)
+        elif action == 'upgrade_book':
+            ans['remove_ncx'] = question_dialog(
+                parent, _('Remove NCX ToC file'),
+                _('Remove the legacy Table of Contents in NCX form?'),
+                _('This form of Table of Contents is superseded by the new HTML based Table of Contents.'
+                  ' Leaving it behind is useful only if you expect this book to be read on very'
+                  ' old devices that lack proper support for EPUB 3'),
+                skip_dialog_name='edit-book-remove-ncx',
+                skip_dialog_msg=_('Ask this question again in the future'),
+                yes_text=_('Remove NCX'), no_text=_('Keep NCX')
+            )
     except Abort:
         return None
     return ans