Reference Manager PDFs to EPUB: Zotero, Mendeley, EndNote, Paperpile and Readwise Reader
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. The same two-copy workflow applies if your library lives in Mendeley, EndNote or Paperpile — only the step of finding the PDF differs, and that is covered below — and if you annotate in Readwise Reader, the EPUB is the better upload.
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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 |
Zotero 7 also opens EPUB files in its built-in reader, so you can attach the converted EPUB to the same item as the PDF and annotate it inside Zotero when you are back at your desk.
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.
Mendeley, EndNote and Paperpile: where the PDF is
Every reference manager keeps the PDF somewhere on disk or in the cloud; the conversion step is the same once you have the file.
| Manager | Where PDFs are stored | Fastest way to get one out |
|---|---|---|
| Mendeley Desktop | ~/Documents/Mendeley Desktop/ (Mac) or C:\Users\[username]\Documents\Mendeley Desktop\ (Windows) | Right-click the reference → Open File Location |
| Mendeley Reference Manager | Elsevier cloud, synced to the desktop and mobile apps | Select the reference → click the PDF attachment in the right panel → download icon |
| EndNote (X7–X9, 20, 21) | MyLibrary.Data/PDF/ next to the .enl library file; on Mac, right-click the library → Show Package Contents | Right-click the reference → PDF → Reveal in Finder / Reveal in Explorer, or Open PDF → Save As |
| Paperpile | Google Drive → My Drive → Paperpile/[Author Year]/ | Right-click the reference → Open PDF → download, or Show in Google Drive; from the Google Docs sidebar, hover a reference → PDF icon |
The reading split is the same as with Zotero: first pass as EPUB on the e-reader or phone; deep annotation in the manager's own reader (Mendeley's reader, EndNote's PDF viewer or iPad app, Paperpile's iOS and Android apps); citations through the Word plugin (Mendeley, EndNote) or the Google Docs plugin (Paperpile). Mendeley, EndNote and Paperpile have no e-reader integration of their own, so the transfer is manual — email to Kindle, USB to Kobo, upload to reMarkable.
Reading and highlighting in Readwise Reader
Readwise Reader is not a reference manager but it is where many researchers do their highlighting. It accepts both PDF and EPUB uploads — upload the EPUB. Highlights on a PDF are tied to fixed page coordinates and text does not reflow; on an EPUB they are clean paragraph-level highlights with font control, a real table of contents and smoother text-to-speech and Ghostreader summaries, because the text is sequential rather than extracted from columns. A scanned PDF cannot be highlighted in Reader at all; its OCR'd EPUB can.
- Convert the PDF at pdf2epub.toolkit.bot and download the EPUB
- Open read.readwise.io (or the iOS/Android app) → + → Upload → choose the EPUB
- Highlight as you read; highlights sync to Readwise and on to Obsidian, Notion, Roam or your notes app
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 — or the Mendeley Desktop folder, an EndNote .Data/PDF folder or a Paperpile Drive 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.
Where does Mendeley store my PDFs?
Mendeley Desktop stores PDFs locally, typically at ~/Documents/Mendeley Desktop/ on Mac or C:\Users\[username]\Documents\Mendeley Desktop\ on Windows; right-click any reference → Open File Location to jump to the file. Mendeley Reference Manager, the newer version, keeps PDFs in the cloud — select the reference, click the PDF attachment in the right panel and use the download icon. Then upload the PDF to pdf2epub.toolkit.bot.
How do I get a PDF out of EndNote?
Right-click the reference → PDF → Reveal in Finder (Mac) or Reveal in Explorer (Windows) to open the folder holding that PDF. Alternatively, PDF → Open PDF, then Save As to keep a copy. The files live in a PDF folder inside MyLibrary.Data next to your .enl file. The same works across EndNote X7, X8, X9, 20 and 21; newer versions add cloud sync but the exported PDF is the same file.
Where does Paperpile store my PDFs?
In Google Drive, in a Paperpile folder at the root of My Drive, with a subfolder per paper named after the first author and year. Get a PDF from the Paperpile web app (right-click → Open PDF → download, or Show in Google Drive), from the Google Docs sidebar (hover a reference → PDF icon → download), or directly from drive.google.com.
Should I upload the PDF or the EPUB to Readwise Reader?
The EPUB. Readwise Reader opens both, but PDF highlights are tied to page coordinates and the text does not reflow, while EPUB gives paragraph-level highlights, font size control, chapter navigation and cleaner input for text-to-speech and Ghostreader summaries. Convert at pdf2epub.toolkit.bot, then in Reader click + → Upload and pick the EPUB; highlights sync to Readwise and to your notes app as usual.