How to Convert Mendeley PDFs to EPUB — Read References on Kindle or Kobo (2026)

Mendeley is a popular reference manager (owned by Elsevier) that stores and organizes your research PDFs. While Mendeley has a built-in PDF reader, reading long journal articles in it on a laptop isn't always the most comfortable experience. Converting papers to EPUB and reading them on a Kindle, Kobo, or phone gives you reflowable text and e-ink comfort — then you return to Mendeley for annotation and citation work.

Free, no account needed. Works in any browser.

Convert Mendeley PDF to EPUB →

How to get a PDF out of Mendeley

Mendeley Desktop (older version)

Right-click the reference → Open File Location — opens the folder containing the PDF
Or: right-click → Open PDF — opens in your default PDF viewer; note the file path from the title bar
Navigate to ~/Documents/Mendeley Desktop/ to browse all stored PDFs

Mendeley Reference Manager (newer web version)

Select the reference in the library
Click the PDF attachment in the right panel
Click the download icon to save the PDF to your computer

Converting and transferring to your e-reader

Go to pdf2epub.toolkit.bot
Upload the Mendeley PDF — conversion takes 30–60 seconds
Download the EPUB
Transfer to your e-reader (Kindle email, Kobo USB, reMarkable app)

Phase	Tool	Device
Discovery and import	Mendeley web clipper or manual import	Computer
First read (absorption)	EPUB converted from Mendeley PDF	Kindle, Kobo, or phone
Deep annotation	Mendeley built-in reader or reMarkable PDF mode	Computer or reMarkable
Note-taking and synthesis	Mendeley notes or linked note app	Computer
Citation insertion	Mendeley Word plugin or BibTeX export	Computer

Frequently asked questions

Where does Mendeley store my PDFs?

Mendeley Desktop stores PDFs in a local folder, typically at ~/Documents/Mendeley Desktop/ on Mac, or C:\Users\[username]\Documents\Mendeley Desktop\ on Windows. You can also right-click any reference in Mendeley → Open File Location to navigate directly to the PDF. Mendeley Reference Manager (the newer web-based version) stores PDFs in the cloud — download them via the web interface or desktop app.

Can I open Mendeley PDFs in my browser?

Mendeley Reference Manager has a built-in browser-based PDF reader. However, this reader doesn't support EPUB export. To convert to EPUB, download the PDF from Mendeley (right-click → Download PDF or Open File Location), then upload to pdf2epub.toolkit.bot. The EPUB version is then transferred to your e-reader separately from your Mendeley workflow.

How does Mendeley compare to Zotero for managing research PDFs?

Both are popular reference managers. Zotero is free and open-source; Mendeley is owned by Elsevier and has a freemium model with cloud storage. Zotero has a more active community and better integration with open-source tools. Mendeley has slightly better integration with Elsevier's ScienceDirect. For PDF-to-EPUB conversion, both work identically — extract the PDF and convert it. The choice between them is about citation management features, not PDF reading.

Should I use Mendeley's built-in reader or read as EPUB on an e-reader?

Mendeley's built-in reader is excellent for annotation and commenting — use it when you're actively working with a paper (extracting quotes, taking notes for a review, adding citations). For the reading pass (absorbing the paper before active work), reading as EPUB on a Kindle or Kobo is more comfortable for long papers. Many researchers use both: read the EPUB first on their commute, then return to Mendeley's reader for annotation.

Does Mendeley Reference Manager work on mobile for reading PDFs?

Mendeley has iOS and Android apps that sync your library and allow PDF reading on mobile. The app works, but reading a two-column journal article on a phone screen is still constrained — the PDF is fixed-layout and requires zooming. Converting to EPUB and reading in Apple Books or Moon+ Reader on the same phone gives much better text reflow and readability.