How to Convert EndNote PDFs to EPUB — Read References on Kindle or Kobo
EndNote is the reference manager of choice in many research institutions, especially in medicine, life sciences, and engineering. It stores your research PDFs locally and optionally in the cloud. Like all reference managers, its built-in PDF viewer is designed for annotation on desktop — not for comfortable reading on e-readers. Converting EndNote PDFs to EPUB fixes this.
What is EndNote?
EndNote is a commercial reference management tool by Clarivate Analytics. It is widely used in academic and research institutions, particularly in medicine, life sciences, and engineering. Key features:
- Import references from PubMed, Web of Science, Cochrane, and most academic databases
- Store and annotate PDFs with a built-in PDF viewer
- Format citations and bibliographies for thousands of journal styles
- Sync library to EndNote cloud (EndNote 20/21 with Sync)
- iPad app for mobile reading and annotation
EndNote is often provided free by universities through institutional license agreements.
Finding PDFs in your EndNote library
EndNote stores PDFs in a local folder structure alongside your library file:
- Mac: Right-click your .enl file → Show Package Contents → open the
PDFfolder. Or: Library menu → .Data/PDF/ - Windows: Navigate to your library folder. Alongside
MyLibrary.enlfindMyLibrary.Data\PDF\
Easiest method: In EndNote, right-click any reference → PDF → Reveal in Finder (Mac) or Reveal in Explorer (Windows). EndNote opens the exact folder containing that PDF.
Converting to EPUB
- Find the PDF: Right-click the reference in EndNote → PDF → Reveal in Finder/Explorer
- Convert: Upload the PDF to pdf2epub.toolkit.bot — takes ~30 seconds
- Download the EPUB
- Transfer to your e-reader: Email to Kindle, USB to Kobo, or upload to reMarkable
Research workflow table
| Task | Best tool |
|---|---|
| Import references from PubMed, Web of Science | EndNote browser extension or direct import |
| Format citations and bibliographies | EndNote → Word plugin |
| Deep annotation and comments | EndNote PDF viewer or iPad app |
| First-pass reading (long papers) | EPUB on Kindle, Kobo, or reMarkable |
| Reading during commute or travel | EPUB on e-reader or phone |
| Systematic review and meta-analysis | EndNote → export to Covidence or Rayyan |
Frequently asked questions
Where does EndNote store my PDFs?
EndNote stores PDFs in a folder called 'PDF' inside your EndNote library package. On Mac, right-click your .enl library → Show Package Contents → find the PDF folder. On Windows, the PDF folder sits alongside your .enl file in the library folder. In EndNote 21 and later with Sync enabled, PDFs are also backed up to EndNote's cloud (EndNote Basic). You can also right-click any reference → PDF → Open PDF to open the file directly.
How do I get a PDF out of EndNote to convert it?
In EndNote, right-click a reference → PDF → Reveal in Finder (Mac) or Reveal in Explorer (Windows). This opens the exact folder containing the PDF. Alternatively, right-click → PDF → Open PDF, then File → Save As or Ctrl+S to save a copy. In EndNote 21 with the new PDF viewer, use File → Export PDF. Once saved, upload to pdf2epub.toolkit.bot for conversion.
Does EndNote have any e-reader integration?
EndNote does not have built-in Kindle or Kobo integration. It has a built-in PDF viewer for annotation, and the iPad app (EndNote for iOS) can be used for reading PDFs on a tablet. For e-reader reading (Kindle, Kobo, reMarkable), the workflow is manual: export the PDF from EndNote, convert to EPUB, then transfer to the device.
Which reference managers work best for e-reader reading workflows?
Zotero, Mendeley, Paperpile, and EndNote all work similarly for the extract-and-convert workflow: find the PDF, download it, convert at pdf2epub.toolkit.bot. Zotero's 'Show File' feature makes finding PDFs fastest. Paperpile stores everything in Google Drive, which is easy to access from any device. EndNote has the most institutional IT support and is common in medical and life sciences. For pure e-reader reading, the reference manager choice doesn't change the workflow — all PDFs convert the same way.
Does EndNoteX9 or earlier work the same way?
Yes. The PDF export workflow is the same across EndNote X9, X8, X7, and the newer EndNote 20/21. The PDF files are always stored in a local folder alongside the .enl library. The main difference in newer versions is cloud sync and an improved PDF viewer — but the exported PDF is the same standard PDF file and converts to EPUB identically.