Background
Most ebooks purchased from major sellers have digital rights management (DRM) applied to them, which means their use is limited in some way. However, there are lots of places to get DRM-free ebooks, including Project Gutenberg, certain ones on Kobo, Humble Bundle, and many publishers who sell their ebooks directly. If those files come in the EPUB format, Kindle users can add them to their libraries using the Send to Kindle feature. They’ll will be categorized as personal documents (Docs in Content Library), but they’ll work like an ebook.
Most DRM-free ebooks will work fine on most readers, but that freedom sometimes has a cost. Kindle readers can be pretty strict about how ebook files are formatted, so files from anywhere but Amazon may sometimes not work perfectly as-is. In my experience, the most common issue is broken footnotes, but text formatting might also be missing. If that happens, you might be able to fix the problem(s) by following these instructions.
Solution
Short Version
- Download and install the calibre ebook management utility (free and open source)
- Import the source EPUB file into calibre
- Convert the EPUB file to AZW3 (an earlier version of Amazon’s Kindle format)
- Export the book in AZW3 format
- Import the AZW3 file as a new book
- Convert the AZW3 file to EPUB format
- Export the book as an EPUB file
- Add the newly-exported EPUB file to your collection via Send to Kindle
Explanation/Longer Version
The idea is to translate the contents of the EPUB file to a Kindle-compatible format by having calibre convert it to a native Kindle one (calibre supports AZW3). At that point, a Kindle should be able to read and display the file correctly. However, Send to Kindle doesn’t support native formats (I think they assume you’ll buy Amazon files from Amazon), so the file has to be converted back to EPUB before it can be uploaded.
I frankly didn’t think this would work the first time I tried it. Anyone who’s done a double translation using an online tool can confirm the results are usually pretty weird. However, since we’re talking about documented file formats rather than the nuances of human language, my experience suggests calibre does actually standardize formatting (and associated functionality) during successive conversions.
I recently ran into issues with I Shall Wear Midnight, the 38th book in the Discworld series by Terry Pratchett. I purchased a Discworld Humble Bundle, and they came in EPUB format. Most of them have worked correctly on my Kindle Paperwhite, but the footnotes (which are frequent and amusing in Pratchett novels) weren’t functional for this one.
I already had calibre installed, but if you don’t, download and install it using the link in the Steps section above. It’s mostly turn-key, but a small thing I recommend: create a folder named calibre somewhere on your computer that’s handy/easy to access (mine is on the root of my D drive), then create two folders underneath named Import and Export. This helps keep things straight. If you’re a big file naming person like me, you’ll probably also want to go to Preferences -> Import/export -> Saving books to disk and create your standard(s). Here are mine, including a manual EPUB format designator at the end since I almost always work with that format nowadays.
Book Not in a Series
{author_sort} – {pubdate} – {title} [EBPUB]
Roach, Mary – 2013 – Gulp; Adventures on the Alimentary Canal [EPUB]
Book in a Series
{author_sort} – {pubdate} – {series} – {series_index:0>2s} – {title} [EBPUB]
Pratchett, Terry – 1996 – Discworld – 19 – Feet of Clay [EBPUB]
All instruction below are based on calibre 9.7 on Windows 11. Future versions may change a bit, but the interface has been pretty consistent for several years. When appropriate, I’ll include specific details of my process for I Shall Wear Midnight as examples. I strongly recommend configuring your file browser to show extensions (.jpg, .png, .epub, etc.) to you’ll be able to tell the difference between EPUB and AZW3 files that have identical names.
Add Source EPUB File and Convert to AZW3
- Make a backup copy of the source EPUB file and save it to a known location just in case
- Move a copy of the source EPUB file to calibre’s Input folder
- I moved ishallwearmidnight.epub to D:\calibre\Input
- Add the source EPUB to calibre by clicking the Add books button in the top menu, navigating to calibre’s Input folder, selecting the source EPUB file, and clicking Open.
- I selected D:\calibre\Input\ishallwearmidnight.epub
- Right-click the book, expand Convert books, and select Convert individually.
- In the output section on the right, change Output format to AZW3.
- Click OK to initiate the conversion. You’ll be notified when the process has completed.
Export AZW3 File and Add as New Book
- Right-click the book, expand Save to disk, and select Save single format to disk.
- Select AZW3 and click OK
- Navigate to calibre’s Output folder and click Select Folder
- When the file has been saved, a File Explorer window will open to the output folder.
- Move the saved AZW3 file from calibre’s Output folder to calibre’s Input folder
- I moved Pratchett, Terry – 2010 – Discworld – 38 – I Shall Wear Midnight [EBPUB].azw3 from D:\calibre\Output to D:\calibre\Input
- Close the File Explorer window
- Back in the main calibre window, delete the entry for the source EPUB book. This is to reduce the risk of errors while performing later tasks.
- Add the converted AZW3 file to calibre by clicking the Add books button in the top menu, navigating to calibre’s Input folder, selecting the converted AZW3 file, and clicking Open.
- I selected D:\calibre\Input\Pratchett, Terry – 2010 – Discworld – 38 – I Shall Wear Midnight [EBPUB].azw3
- Make any desired metadata changes by right-clicking the book, expanding Edit metadata, and selecting Edit metadata individually. When, you’re done, click OK.
- I changed the Author Sort to Pratchett, Terry, confirmed the Published date, entered Discworld as the Series, and added 38 as the Number.
Convert AZW3 File to EPUB
- Right-click the book, expand Convert books, and select Convert individually.
- In the output section on the right, change Output format to EPUB and confirm the metadata before clicking OK.
- When the conversion has completed, right-click the book, expand Save to disk, and select Save single format to disk.
- Select EPUB and click OK
- Navigate to calibre’s Output file (if it’s not already selected) and click Select Folder
- File Explorer should again open to calibre’s Output file to show the exported files, including the converted EPUB file.
- Mine was D:\Calibre\Output\Pratchett, Terry – 2010 – Discworld – 38 – I Shall Wear Midnight [EBPUB].epub
You’ll be able to upload the converted EPUB file via Send to Kindle, and formatting like chapter headers, italicized/bolded text, and footnote links should now work as expected.

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