How to Convert Zotero PDFs to EPUB — Read Your Reference Library on Any E-Reader (2026)
Zotero is the most popular free reference manager for researchers — it stores PDFs, manages citations, and has a built-in annotation reader. But reading long papers on a laptop isn't always comfortable. Converting your Zotero PDFs to EPUB lets you read them on a Kindle, Kobo, or phone, then return to Zotero for annotations and citation work.
Free, no account needed. Works in any browser.
Convert Zotero PDF to EPUB →The workflow: Zotero + EPUB reading
- Find the PDF in Zotero: Right-click the item → Show File. This opens the folder containing the PDF in your file manager.
- Convert at pdf2epub.toolkit.bot: Upload the PDF, wait ~30 seconds, download the EPUB.
- Transfer to your e-reader: Email to Kindle, USB drag-and-drop to Kobo, or upload to reMarkable app.
- Read and take light notes on your device.
- Return to Zotero for serious annotation, citation insertion, and note organization.
Two-copy workflow
| Task | Where to do it |
|---|---|
| First pass reading (long papers) | EPUB on Kindle, Kobo, or reMarkable |
| Deep annotation and margin notes | Zotero PDF reader or reMarkable PDF mode |
| Citation lookup and page numbers | Zotero PDF (fixed page numbers) |
| Note organization and connection | Zotero notes or linked note-taking app |
| Bibliography export | Zotero → Word, LaTeX, or Google Docs |
Finding your PDFs in Zotero storage
If you use Zotero's default file storage (not WebDAV or linked files):
- Mac:
~/Zotero/storage/[random-folder]/ - Windows:
C:\Users\[username]\Zotero\storage\[random-folder]\ - Linux:
~/.zotero/zotero/[profile]/zotero/storage/[random-folder]/
The easiest way to find a specific paper: right-click the Zotero item → Show File. Zotero opens the folder in your file manager.
Batch conversion for large Zotero libraries
If you want to convert many PDFs at once, the toolkit.bot API accepts HTTP POST requests with PDF files and returns EPUBs. A short Python script can walk your Zotero storage folder and convert every PDF automatically. See the API docs at toolkit.bot/docs.
Frequently asked questions
Where does Zotero store my PDFs?
Zotero stores attached PDFs in its data directory, typically at ~/Zotero/storage/ on Mac/Linux or C:\Users\[username]\Zotero\storage\ on Windows. Each attachment is in a subfolder with a random 8-character name. You can find a specific PDF by right-clicking the item in Zotero → Show File. Alternatively, use Zotero's 'Open PDF' function to open it, then find the file path in your OS.
Can I convert PDFs directly from Zotero's built-in reader?
Zotero's built-in PDF reader is good for annotation, but it doesn't export to EPUB. To convert, locate the PDF file (right-click item → Show File), then upload it to pdf2epub.toolkit.bot. The conversion is separate from Zotero — you then read the EPUB on your e-reader and continue using Zotero for annotations and citation management.
Should I keep the PDF in Zotero after converting to EPUB?
Yes — keep both. Zotero's PDF is your primary reference for citation (Zotero reads metadata, DOI, and page numbers from PDFs). The EPUB is your reading copy. This two-copy workflow is standard for researchers: read and annotate with a pen on reMarkable or Kindle Scribe, do serious annotation and citation lookup in Zotero on your computer.
Can I sync my Zotero annotations with what I highlight in the EPUB?
Not automatically — Zotero and EPUB readers are separate systems. Some researchers use a manual workflow: read and highlight in the EPUB reader, then return to the PDF in Zotero to add the same highlights as Zotero annotations for citation lookup. Apps like Readwise can import highlights from Kindle and some other readers and help bridge this gap if you use Kindle to read the EPUB.
Is there a way to batch-convert all my Zotero PDFs to EPUB?
The pdf2epub.toolkit.bot API supports batch conversion via HTTP POST requests. You can write a short Python script that reads your Zotero storage directory, finds PDFs, and calls the API for each one. The API returns the EPUB which you can save alongside the PDF. See the API documentation at toolkit.bot/docs.