You drag an EPUB into Calibre and get an error. Maybe "Saving a book based on a folder is not supported." Maybe the import just silently fails. The file looks fine in Finder — it has an .epub extension — but Calibre won't touch it.
This is almost always an Apple Books problem.
What went wrong
EPUB files are ZIP archives with a specific structure. When Apple Books imports an EPUB, it unpacks it into a folder of loose files. If you later export or copy that book out of Apple Books, you sometimes get the raw folder back — not a proper ZIP archive.
The file still has an .epub extension, but it's actually a directory pretending to be a file. Calibre's creator Kovid Goyal has confirmed this directly: Apple stores ebooks as "folders whose name ends with .epub."
Calibre expects a real ZIP archive, not a folder. So it rejects it.
How to check if your EPUB is broken
On a Mac, right-click the file and select "Show Package Contents." If it opens and shows you a folder full of files (like META-INF, OEBPS, mimetype), your EPUB is a directory — not a valid archive.
A proper EPUB won't open with "Show Package Contents." It's a single compressed file.
How to fix it
Option 1: EPUB Fixer (fastest)
Upload the broken file and get a valid EPUB back in seconds:
- Go to EPUB Fixer
- Drop your file
- Download the fixed version
- Import into Calibre — it will work
The tool repackages everything into a proper ZIP archive with the correct structure: uncompressed mimetype as the first entry, everything else compressed. No installation, no account needed.
Option 2: Repackage manually
If you're comfortable with the terminal:
cd /path/to/broken-book.epub
zip -X0 ../fixed-book.epub mimetype
zip -rX9 ../fixed-book.epub . -x mimetype
This creates a new EPUB with the correct ZIP structure. The -X0 flag stores mimetype without compression (required by the EPUB spec), and -rX9 compresses the rest.
Option 3: Re-download the original
If you purchased the book from a DRM-free store, download the original file again. The store's version will be a proper EPUB. Avoid importing it into Apple Books if you plan to use it with Calibre.
Want to send it straight to Kindle?
Once your EPUB is fixed, you can transfer it from Apple Books to your Kindle using email, USB, or the Send to Kindle app. Or use PaperDrop — a Telegram bot that delivers EPUBs and PDFs directly to your Kindle. Send it a broken Apple Books EPUB and it'll fix the file and deliver it — no manual steps needed. It also converts web articles and PDFs to Kindle format.
Why this only happens with Apple Books
Other reading apps (Kobo, Google Play Books) keep EPUBs as single files. Apple Books is unique in unpacking them into directory structures. This is fine within Apple's ecosystem — the Books app reads folders just fine — but it breaks compatibility with everything else.
It's not malicious. It's just how Apple chose to store ebook data internally. The problem is that macOS still labels these folders with the .epub extension, which makes them look like valid files to users.
Preventing it in the future
- Keep original EPUB files in a separate folder. Don't rely on Apple Books as your only copy.
- Use Calibre as your primary library manager if you read across multiple devices.
- If you must use Apple Books, always keep the original file backed up before importing.
If you've already lost the originals and Apple Books is your only copy, EPUB Fixer will get them back into a format Calibre can read.