Every footnote or endnote in your manuscript passes through three stages before a reader sees it: your authoring tool (Word, Vellum, Atticus, or InDesign), the export format (EPUB, PDF, or .docx), and the reading platform (Kindle, Apple Books, Kobo, Nook, or Google Play). Formatting decisions you make at stage one determine what readers experience at stage three. This guide walks through each authoring tool and shows you exactly what to do based on where you plan to publish.
What Readers See on Each Platform
Before choosing a workflow, you need to know what the reader will actually experience. In print, footnotes appear at the bottom of the page and endnotes collect at the back of the book or end of the chapter; both work exactly as expected. Ebooks are where the variation starts, because reflowable text has no fixed page and therefore no “bottom of the page” to put a footnote on.
The EPUB3 specification introduced a mechanism for ebook footnotes: the <aside epub:type="footnote"> element paired with an <a epub:type="noteref"> link. Reading systems that recognise this markup can show the note as a pop-up overlay. Those that do not recognise it treat the note as ordinary HTML content, displaying it as a linked endnote instead. This is a progressive enhancement: the pop-up is the upgraded experience, but the endnote with bi-directional links is the baseline that works everywhere.
Here is how each major platform handles notes when your EPUB contains correct EPUB3 markup and bi-directional links:
Kindle (KDP): Pop-up overlay. The reader taps a superscript number; the note appears in a floating panel. Tapping outside the panel returns them to the text. KDP’s guidelines require bi-directional hyperlinks; without them, the pop-up may not appear and the reader is sent to the endnotes section with no return link.
Apple Books: Pop-up overlay. Apple has the most mature implementation; the Books Asset Guide documents the required markup structure. Notes appear as tappable overlays on all Apple devices.
Google Play Books: Pop-up overlay on Android and iOS apps.
Kobo: Pop-up overlay on newer devices and apps. Older e-ink Kobo readers do not support pop-ups; they fall back to displaying the note as a linked endnote at the end of the chapter. The bi-directional links let the reader jump to the note and back.
Nook: No pop-up support. Notes always appear as linked endnotes. Bi-directional links are essential here; without the return link, the reader has no way back to their place in the text.
The practical takeaway: if you format your notes with EPUB3 markup and bi-directional links, readers on pop-up-capable platforms get the overlay experience, while readers on other platforms get functional linked endnotes. You do not need separate files for different platforms. The same EPUB works everywhere; only the presentation changes.
Microsoft Word
Most manuscripts start in Word, even if they are later formatted in another tool. Word’s built-in footnote and endnote system (References tab > Insert Footnote or Insert Endnote) handles numbering automatically. Footnotes appear at the bottom of each page; endnotes collect at the end of the section or document, depending on the setting in the Footnotes dialog. Both use the same superscript numbering and can be converted to the other format at any time (see “How do I convert footnotes to endnotes in Microsoft Word?” in the FAQ below).
Word does not produce EPUB files directly; it produces .docx or PDF. This means Word is almost always stage one of a two-stage process: you author in Word, then either upload the .docx to a retailer that converts it, or you run the file through a dedicated formatting tool that produces the EPUB.
If you are uploading .docx directly to KDP
KDP accepts .docx files and converts them to Kindle format automatically. The conversion engine will attempt to turn your Word footnotes into pop-up notes with bi-directional links. The results are inconsistent: some manuscripts convert cleanly, others lose the return links or produce duplicate note markers. If you upload to KDP this way, preview the converted file in Kindle Previewer before publishing and check that every note opens as a pop-up and that you can return to the text.
This path only produces a Kindle ebook. It does not give you an EPUB for Apple Books, Kobo, or other platforms.
If you are publishing on multiple platforms (wide distribution)
You need an EPUB file, and Word cannot produce one on its own. The most common workflows are:
Word → Vellum: Import your .docx into Vellum (see the Vellum section below). Vellum reads Word’s footnote markers and converts them automatically. This is the path with the least manual work.
Word → Atticus: Import your .docx into Atticus. Atticus reads Word footnotes, but they must be in Word’s default footnote style (not endnotes). If your manuscript uses endnotes, convert them to footnotes in Word first: References tab > dialog launcher arrow > Convert > “Convert all endnotes to footnotes.”
Word → Calibre or Sigil: Convert .docx to EPUB using Calibre, then clean up in Sigil. This is a manual process that gives you full control but requires familiarity with EPUB structure and HTML/CSS.
Print and ebook from one Word file
Keep footnotes in your Word master file for print. When it is time to produce the ebook, make a copy of the file (never modify the master) and either import the copy into Vellum/Atticus or convert footnotes to endnotes in the copy using the References tab conversion tool. If you are working with a professional formatter, provide the master with footnotes and specify that you want endnotes with bi-directional links in the ebook. For more on managing dual formats, see producing both a paperback and ebook from one Word manuscript.
Vellum
Vellum (Mac only; $249.99 for print + ebook) handles the print-to-ebook note problem with the least author intervention of any tool. You insert a footnote in the text editor; Vellum does the rest.
What Vellum produces
Print: Footnotes appear at the bottom of the page. Endnotes (a separate Vellum feature) appear at the back of the book. You choose between them per note or convert all at once using the gear menu in the note editor.
Ebook: Vellum generates EPUB3 files with the aside epub:type="footnote" markup and bi-directional links. On Kindle, Apple Books, and Google Play, readers see a pop-up overlay. On Kobo (older devices) and Nook, where pop-ups are not supported, the same file falls back to displaying notes as linked endnotes at the end of the chapter. The reader can tap the note number to jump to the note, and a return link brings them back. Vellum builds both the pop-up layer and the endnote fallback into every EPUB it generates; you do not need to configure this.
If you are publishing on KDP only
Generate a Kindle-specific file from Vellum (File > Generate Books > select Kindle). The output is a .mobi-compatible package that KDP accepts directly. Pop-up notes work on all Kindle devices and apps.
If you are publishing wide
Generate platform-specific files (Apple, Kobo, Nook, Generic) or a single “Generic” EPUB for aggregators like Draft2Digital. Keep EPUB3 output enabled in Generation Settings; this preserves the pop-up markup for platforms that support it while maintaining the linked-endnote fallback for those that do not. One file covers all platforms.
Print and ebook from one Vellum project
This is Vellum’s default workflow. The same project file produces a print PDF with footnotes at the page bottom and an ebook with pop-ups or linked endnotes, depending on the reader’s device. No conversion step, no separate file.
Vellum offers four indicator styles: symbols (*, †, ‡), numbers (1, 2, 3), roman numerals (i, ii, iii), and letters (a, b, c). The symbol style is the default and suits books with a few notes per chapter; numbered indicators are better for heavily annotated non-fiction. For more on Vellum’s footnote handling, see Vellum’s footnote documentation.
Atticus
Atticus ($147 one-time; Mac, Windows, Linux, Chromebook) gives you explicit control over where notes appear in each format. Unlike Vellum, which decides placement automatically, Atticus asks you to choose.
What Atticus produces
Print: Three options in the Formatting tab: footnotes (bottom of the page), end-of-chapter notes, or end-of-book notes.
Ebook: Since reflowable ebooks have no page bottom, the footnote option is not available for ebook export. You choose between end-of-chapter and end-of-book placement. Atticus generates bi-directional hyperlinks in both cases: readers tap the superscript to jump to the note and a return link to get back. The notes display as linked endnotes at the chapter or book level. Whether Kindle or Apple Books presents them as pop-up overlays depends on the EPUB markup Atticus includes in the export; check the preview on your target platform to confirm the presentation.
If you are publishing on KDP only
Export from Atticus and upload the EPUB to KDP. Choose end-of-chapter or end-of-book placement based on your book’s structure. End-of-chapter tends to work better for books with many notes; end-of-book is cleaner for books with occasional citations.
If you are publishing wide
The same EPUB works across platforms. The bi-directional links ensure navigation works on every reader. On platforms that support pop-ups, readers may get the overlay experience; on those that do not, they get the linked endnote experience. Either way, the notes are accessible and navigation works.
Print and ebook from one Atticus project
Set note placement to “Footnotes” for print and “End of Chapter” or “End of Book” for ebook in the Formatting tab. Atticus handles the split when you export each format from the same project.
Importing from Word
Atticus imports footnotes from Word’s .docx format, but the notes must be in Word’s default footnote style. If your Word manuscript uses endnotes, convert them to footnotes in Word before importing (References tab > Convert > “Convert all endnotes to footnotes”). Each note must be under 1,000 characters in Atticus, and empty note markers will cause export issues. Check for both before uploading a heavily annotated manuscript.
Adobe InDesign
InDesign is the most powerful option for footnote and endnote formatting, and the most complex. It is typically used by professional typesetters rather than authors working on their own layouts.
What InDesign produces
Print: Full footnote support with extensive typographic control (positioning, ruling, spacing, numbering restarts). InDesign’s print footnote feature is the most configurable of any tool covered here.
Ebook: When exporting to EPUB, InDesign’s footnote placement options include: append to end of section, place after the referencing paragraph, or display as a pop-up. The pop-up option generates EPUB3-compliant aside markup with bi-directional links. On readers that support pop-ups, the note appears as an overlay; on those that do not, the note falls back to a linked endnote at the section level.
If you are publishing on KDP only
Export to EPUB3 with the pop-up footnote option selected. Upload the EPUB to KDP. Kindle will display the notes as pop-ups.
If you are publishing wide
Use the same EPUB3 export. The pop-up markup provides the overlay experience on capable platforms and the linked-endnote fallback on others. For wide distribution through IngramSpark or aggregators, the EPUB passes through to retailers without modification.
Print and ebook from one InDesign file
Maintain footnotes in the InDesign file for print PDF export. For EPUB export, use the “popup” footnote option or, for complex academic books with hundreds of notes, convert to endnotes using Peter Kahrel’s footnote-to-endnote conversion script. The script creates dynamic endnotes with cross-reference links, which is often necessary for EPUB export of heavily annotated manuscripts where InDesign’s native conversion is limited.
Common Footnote Formatting Mistakes
Missing return links. The note reference in the text links to the endnote, but the endnote does not link back. On Kindle, the pop-up may not appear; on Nook, the reader gets stranded in the endnotes section with no way back. KDP’s quality checks flag one-directional links as a content warning. Every formatting tool covered in this guide generates bi-directional links automatically; this problem most often arises when authors build EPUB files manually or upload a .docx to KDP without checking the preview.
Manual footnotes instead of the built-in system. Some authors type footnote numbers and text at the bottom of each page in Word rather than using Insert Footnote. These “fake” footnotes carry no structural metadata, so no formatting tool or retailer can convert them to functional ebook notes. They also do not renumber when you add or remove a note. Always use the built-in footnote or endnote feature in whatever tool you write in.
Mixing footnotes and endnotes in the same manuscript. A manuscript should use one system or the other. Mixed numbering confuses readers and creates unpredictable results during ebook conversion.
Footnotes in fiction. If your novel uses footnotes as a literary device (in the style of Terry Pratchett or Susanna Clarke), test the ebook version on multiple devices before publishing. The pop-up presentation works well for short asides but can feel disruptive if notes are very frequent. Some fiction authors convert literary footnotes to inline parenthetical text for the ebook edition.
Empty note markers. Deleting the text of a footnote in Word without deleting the superscript marker leaves a blank note that can cause export failures in Atticus and display problems on Kindle. Search your manuscript for empty note markers before exporting.
Endnotes are part of your book’s back matter structure. Planning where the endnotes section sits relative to your bibliography, acknowledgements, and about-the-author page produces a more natural reading experience than treating notes as an afterthought. If your EPUB passes validation on one platform but produces errors on another, the note linking structure is one of the first things to check.
Frequently Asked Questions
If I format footnotes for pop-ups, will readers on Nook or older Kobo devices still see the notes?
Yes. EPUB3 pop-up footnotes are a progressive enhancement, not an either/or choice. Readers on platforms that support pop-ups (Kindle, Apple Books, Google Play, newer Kobo) see an overlay. Readers on platforms that do not (Nook, older Kobo e-ink) see the same notes displayed as linked endnotes at the end of the chapter. The bi-directional links ensure navigation works in both cases. You do not need separate files for different platforms.
Can I use footnotes in a Kindle ebook?
Yes. Kindle displays footnotes as pop-up overlays when the file contains bi-directional hyperlinks and EPUB3 markup. The reader taps the superscript number, reads the note in a floating panel, and taps outside to return. If the links are missing or one-directional, the pop-up may not appear and the reader is sent to an endnotes section instead. Vellum, Atticus, and InDesign all produce Kindle-compatible footnote markup automatically.
Should I use footnotes or endnotes for a non-fiction ebook?
For ebooks, endnotes with bi-directional links are the safest universal format because they work on every reading platform without relying on pop-up support. However, if you use Vellum, you can write with footnotes in your manuscript and Vellum will handle the conversion to pop-ups (on supported readers) and linked endnotes (on others) automatically. The key requirement is that readers can navigate to the note and back regardless of their device.
How do I convert footnotes to endnotes in Microsoft Word?
Open the References tab, click the small dialog launcher arrow at the bottom-right of the Footnotes group, then click the Convert button. Select “Convert all footnotes to endnotes” and click OK. Word preserves numbering and content. This feature is only available in the desktop application; Word Online does not support footnote conversion.
Do I need different EPUB files for different platforms?
No. A single EPUB3 file with bi-directional links works on all platforms. The reading platform determines the presentation: pop-up overlay where supported, linked endnotes where not. If you use Vellum, you can optionally generate platform-specific files for Kindle, Apple, Kobo, and others, but a single “Generic” EPUB also works for aggregator distribution through Draft2Digital or IngramSpark.
