Converting InDesign and Affinity Publisher PDFs to EPUB: The Complete Guide
Built your book in InDesign or Affinity Publisher? Learn the safest PDF‑first workflow to convert your designs into Kindle‑ready fixed‑layout EPUBs without losing fonts, images, or page structure.
By Magnus | Published 2026-04-16 | Category: Guide
InDesign's native EPUB export works, but it requires complex per-object
configuration and frequently breaks designed layouts. Affinity Publisher
has no native EPUB export at all. The better approach for both tools:
export a PDF/X-4 from your design software, then convert that PDF to
fixed-layout EPUB using
MJ Convert Systems. You get 99.7% layout accuracy
without touching EPUB code.
Why InDesign's Built-In EPUB Export Often Breaks Layouts
Adobe InDesign has two built-in EPUB export routes: reflowable and
fixed-layout. The reflowable route is the default and is fine for
text-heavy books. The fixed-layout route can produce a good result, but
it demands a significant amount of manual preparation.
To produce a correct fixed-layout EPUB from InDesign natively, you
need to:
- Tag every text frame and image frame individually with the correct
export settings
- Set reading order manually using the Articles panel — otherwise
screen readers and some Kindle apps read content in the wrong order
- Configure each image as absolutely positioned within the layout
rather than anchored inline
- Handle master page elements separately, as they are not always
exported correctly
- Test on multiple Kindle devices to catch rendering differences between
the Kindle app on iOS, Android, and dedicated e-ink devices
For a 20-page children's book, this is manageable. For a 300-page
cookbook with varied layouts on every spread, it's an enormous amount
of work — and a single mis-tagged frame can break an entire chapter.
Why Affinity Publisher's Export Is Even More Limited
Affinity Publisher does not currently have a native EPUB export feature.
This is a known limitation of the application. The export options
available are PDF, PDF/X, SVG, PNG, JPEG, and EPS — none of which are
valid for Kindle upload without further conversion.
This means that every Affinity Publisher user who wants to publish an
eBook must use a PDF-to-EPUB conversion step. The only question is
which converter to use.
Free tools like Calibre convert PDFs to reflowable EPUB, which destroys
designed layouts. The correct approach is to convert to fixed-layout
EPUB, which preserves the exact positioning of every element. See our
comparison of
Calibre vs MJ Convert Systems
for a detailed breakdown of the difference.
The PDF-First Workflow — Why It's Actually Better
The PDF-first workflow has a counterintuitive advantage: InDesign's and
Affinity Publisher's print PDF export pipelines are both mature,
extensively tested, and produce highly reliable output. The print PDF
pipeline has been refined over decades. The EPUB export pipeline is
much newer and less battle-hardened.
Here's what the PDF-first workflow looks like in practice:
- Design your book in InDesign or Affinity Publisher as normal —
no changes needed to your existing workflow
- Export a high-quality PDF using the settings detailed below
- Upload the PDF to
MJ Convert Systems
- The automated audit checks the file for compatibility issues
- Fixed-layout EPUB conversion preserves your design exactly
- Download your EPUB and upload directly to KDP
The entire conversion process — from upload to download — typically
takes under ten minutes for a standard 200-page book. Compare that to
several hours of manual EPUB configuration in InDesign with uncertain
results.
How to Export the Perfect PDF from InDesign
The quality of your EPUB conversion depends heavily on the quality of
the source PDF. These settings produce a PDF that converts cleanly and
accurately.
Use the PDF/X-4 preset
Go to File → Export → Adobe PDF (Print). From the Preset dropdown,
choose PDF/X-4. This preset enables PDF transparency (unlike PDF/X-1a
which flattens everything) and supports modern colour management.
Embed all fonts
In the PDF export dialog, go to Output → Advanced. Ensure "Subset
fonts below 100%" is set. Fonts must be embedded — not just referenced
— or the Kindle renderer will substitute them, causing text drift.
Set colour output to RGB
InDesign often defaults to CMYK colour output. Kindle displays are
RGB-only. In the Output tab of the PDF export dialog, set Colour
Conversion to "Convert to Destination" and choose "sRGB
IEC61966-2.1" as the destination profile.
Deselect spreads
In the General tab, make sure "Spreads" is not
ticked. Each page must export as a single page, not as a two-page
spread. Fixed-layout EPUB handles individual pages — spreads will be
treated as single wide pages and appear incorrectly on Kindle.
Set bleed to 0
Unless your design specifically requires bleed for a print-on-demand
edition, set bleed to 0 on all sides. Bleed areas are outside the
reading area and add unnecessary content to the EPUB conversion.
Do not apply password or DRM
PDF passwords and DRM settings prevent automated tools from reading
the file during conversion. Export without any security settings.
How to Export the Perfect PDF from Affinity Publisher
Affinity Publisher's PDF export is accessed via File → Export → PDF.
The settings are slightly different from InDesign but follow the same
principles.
Select PDF (Digital — High Quality)
Affinity Publisher offers several PDF presets. Choose "PDF
(Digital — High Quality)" or create a custom preset with the following
settings.
Compatibility: PDF 1.6 or higher
Set compatibility to PDF 1.6 or PDF 1.7. Earlier versions have limited
transparency support and may not embed fonts correctly.
Export as individual pages
In the Pages section, choose "All Pages" and ensure "Export as
single pages" is enabled. If your document uses facing pages, this is
especially important.
Embed fonts
Under the Fonts section, enable "Embed fonts". If you are using any
system fonts that cannot be embedded due to licensing restrictions,
convert text to outlines before export — but be aware this prevents
text from being searchable in the final EPUB.
Rasterise DPI
Set the rasterisation DPI to 300. This ensures that any effects
(shadows, blurs, transparency) are rasterised at a resolution that
looks sharp on Kindle HD displays.
Converting Your PDF to Fixed-Layout EPUB
With a well-formed PDF in hand, the conversion process is
straightforward.
Upload your PDF to
MJ Convert Systems. The platform runs a
pre-flight audit that checks:
- Font embedding status (every font, every page)
- Colour space (flags CMYK content and converts automatically if
possible)
- Page dimensions and viewport compatibility
- Image resolution (minimum 150 DPI for conversion, 300 DPI recommended)
- Transparency and blending mode compatibility
- Spread detection (automatically splits if needed)
Any issues are flagged with specific page numbers and recommended
fixes before conversion begins. This prevents wasted conversion
attempts on files that will produce poor output.
Once the audit passes, conversion produces a fixed-layout EPUB with
99.7% layout accuracy. Visual validation checks every page before
the file is released for download. The drift score — the measure of
how far any element has moved from its position in the original PDF —
is targeted at 0.3% or less.
See our guide to
fixed-layout vs reflowable EPUB
for a detailed explanation of how fixed-layout EPUB works and why it's
the correct format for designed books.
Common Issues Specific to InDesign and Affinity Publisher PDFs
Master page elements not exporting correctly
InDesign master page elements — running headers, page numbers, background
decorations — sometimes export without correct bounding box information.
This causes them to be mispositioned in the converted EPUB. The
pre-flight audit catches this and flags the specific elements.
The fix is to override master page items on the affected pages in
InDesign (right-click the item → "Override Master Page Item"), then
re-export. This gives each element an independent bounding box that
survives conversion.
CMYK colour shift
If you've been working in CMYK (common for designers who also produce
print editions), the colour conversion to RGB sometimes produces
unexpected results — particularly with deep blacks, Pantone spot
colours, and certain muted tones. Always check colour after conversion
by reviewing the visual validation output before publishing.
Linked vs embedded images in InDesign
InDesign can work with linked images (the original files live on disk)
or embedded images. When exporting to PDF, make sure all linked images
are present and correctly linked — InDesign will warn you if any links
are broken. If a linked image is missing, it exports at low resolution
from the display proxy, which looks poor in the final EPUB.
Spread-formatted documents
If your InDesign document was set up with facing pages (as most book
documents are), ensure you export individual pages — not spreads. A
spread exported as a single page will appear as an extremely wide
landscape page in the EPUB, which is not what you want.
Affinity Publisher text on path
Text placed on a path in Affinity Publisher (circular text, text
following a curve) sometimes exports to PDF as outlines rather than
live text. This is fine for layout preservation — the visual result is
identical — but the text will not be searchable in the EPUB. If
searchability matters, keep text-on-path effects minimal.
- Calibre vs MJ Convert Systems comparison
- Fixed layout vs reflowable EPUB
- How to fix page misalignment on KDP
- MJ Convert Systems PDF to EPUB converter
- See pricing and plans starting from $17.97/month
- See more guides on converting PDFs to Kindle
Frequently Asked Questions
- Why doesn’t InDesign’s built-in EPUB export preserve my layout?
- InDesign’s EPUB (Reflowable) export produces a reflowable EPUB by default, where the reading device controls element positioning. Fixed-layout EPUB requires careful manual configuration.
- Does Affinity Publisher have a native EPUB export?
- No. As of the current version, Affinity Publisher does not export to EPUB directly. Export a PDF and convert it to fixed-layout EPUB.
- What PDF export settings should I use in InDesign for eBook conversion?
- Use PDF/X-4. Enable ‘Embed all fonts’. Set colour space to RGB (not CMYK). Set bleed to 0 unless your design uses bleed. Flatten all transparency.
- Can I convert a file with facing pages / spreads to EPUB?
- Yes, but spreads should be split into individual pages before conversion. MJ Convert Systems also detects and handles spread-formatted PDFs automatically.
- InDesign uses CMYK. Does that cause problems for Kindle?
- Yes. Kindle displays are RGB-only. CMYK PDFs may have colour shift when converted. MJ Convert Systems handles CMYK-to-RGB conversion automatically.
- What’s the difference between converting an InDesign EPUB export and converting an InDesign PDF?
- The PDF-first approach produces a single well-structured file from InDesign’s print pipeline, then lets a dedicated converter handle the EPUB packaging — typically producing better results with less manual work.
See more guides on converting PDFs to Kindle
MJ Convert Systems PDF to EPUB converter
See pricing and plans starting from $17.97/month
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