How to Format a Scrivener Manuscript for Kindle Direct Publishing

Scrivener's Compile feature can produce a clean, KDP-ready file. It can also produce one with vanished scene breaks, a stripped table of contents, or a font that isn't what you set, and the difference usually comes down to a handful of specific settings most writers never dig into until something goes wrong.

Export .epub, not .mobi

Amazon stopped accepting .mobi files for KDP uploads in March 2025. Upload an .epub instead, and Amazon converts it internally using its own process, which is more consistent than routing through Scrivener's older .mobi export path. If you've been exporting .mobi out of habit, switching to .epub alone resolves a chunk of formatting inconsistency.

Fix scene breaks that go missing

A scene break that's just a blank line in your manuscript can get silently collapsed during ebook conversion, since a blank line isn't a real structural marker as far as the converter is concerned. In Compile settings, assign an actual separator, a centered symbol like *** configured as a Section Break rather than left as plain text, to every scene division. That gives the converter something explicit to preserve.

Understand why fonts don't always come through

Scrivener's ebook output doesn't reliably embed fonts, and in some export paths it strips font-face information entirely, meaning the book falls back to whatever default font the reading device uses. This isn't usually a setting you can fix inside Scrivener; it's a limitation of its ebook conversion path. If font control matters for your project, exporting to Word first and converting through a dedicated tool like Calibre often produces a more predictable result than Scrivener's direct export.

Watch your table of contents

Scrivener can auto-generate a clickable table of contents on Windows exports. If you've built a manual table of contents instead, Compile can strip the links out of it during conversion, leaving a table of contents that looks right but doesn't function. Stick with the auto-generated version unless you have a specific reason not to.

Test on an actual device before you publish

Line spacing and margins that look correct in Scrivener's preview can render differently once they hit a real Kindle. Amazon's own Kindle Previewer tool, or uploading a draft to KDP and checking it before publishing live, catches problems a desktop preview alone won't show you.

If this feels like more setup than it should be

None of this is unusual for Scrivener specifically; export configuration is simply part of how Compile works, and getting it right the first time takes real setup effort. It's also exactly the step a fiction-specific tool with a single, fixed export path skips entirely. Quillen's export to Word and PDF applies the same industry-standard formatting shown on screen, with no compile settings, no separate ebook conversion pass, and no font-embedding step to configure, since the manuscript editor never leaves that formatting in the first place.