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EndNote is licensed, not free — a standalone license runs $275, a verified-student license $150, and an upgrade from an older version $125, all as one-time purchases direct from Clarivate (site/volume licensing is custom-quoted). For most researchers who ever leave EndNote, the trigger isn’t a subscription lapsing — EndNote’s individual licenses aren’t subscriptions — it’s an institutional or site license ending: graduation, a job change, or a university switching its licensed reference-manager vendor. Whatever the trigger, the question is the same: what can you actually move your library into, and what survives the move.
This page covers three real destinations — Zotero, Mendeley, and JabRef — what each one costs, how you get your EndNote references into it, and what specifically breaks in that transfer. If you haven’t decided a destination yet, see Zotero vs. EndNote vs. Mendeley for a fuller feature comparison first; this page assumes you’re leaving EndNote and need the mechanics.
The three alternatives, compared
| Tool | Cost | Word processor support | Best fit |
|---|---|---|---|
| Zotero | Free core product; optional cloud storage from $20/year (2 GB) to $120/year (unlimited); 300 MB free tier | Word, LibreOffice/OpenOffice, and the only one of the three with a native, official Google Docs plugin | Anyone who writes in Google Docs, or wants a free, open-source tool with no institutional dependency |
| Mendeley | Free; Elsevier-owned, commonly reported around 2 GB free storage | Mendeley Cite supports Microsoft Word only — no official Google Docs support | Researchers already inside the Elsevier/ScienceDirect ecosystem who stay in Word |
| JabRef | Free, open-source | Not a Cite-While-You-Write tool for Word; it manages a .bib file for LaTeX (BibTeX/BibLaTeX) workflows |
Researchers writing in LaTeX/Overleaf rather than Word or Google Docs |
None of the three read EndNote’s native .enl library file directly — .enl is a proprietary EndNote database format paired with a same-named .Data folder that holds attachments and the full-text index, and it isn’t something other reference managers parse. Every migration path below starts the same way: export from EndNote into an interchange format first.
Getting your references out of EndNote
In EndNote, File > Export lets you write your library (or a selected group) out as a plain reference-interchange file rather than the native .enl database. The two formats that matter for migration are the same two covered on CASRAI’s RIS file format guide and demonstrated for the reverse direction on Exporting a Zotero Library into EndNote:
- RIS — the older, simpler, widely-read plain-text interchange format. References only; no file attachments travel through an RIS export, and any italic, bold, or other in-field formatting is lost on the way through. RIS also has no concept of EndNote’s Groups — a flat RIS file arrives in the destination tool as one undifferentiated list.
- XML — EndNote’s own richer export format. It’s the format Zotero’s own documentation recommends specifically because it can carry file attachments along, provided the export is handled correctly (see below) — at the cost of a more fragile import than RIS.
Whichever format you use, export by group or subset where practical rather than your whole library in one pass — none of the three destinations reliably reconstruct EndNote’s Group structure automatically, so working in smaller, already-organized chunks is the difference between arriving with usable folders and arriving with one 3,000-reference pile you have to re-sort by hand.
Zotero: the best-documented path
Per Zotero’s own import documentation, Zotero cannot read .enl directly, and its recommended export format is XML, not RIS — the opposite of the “RIS is the safe default” advice that applies to most other reference-manager migrations. The mechanics matter: export the XML file into your My Documentsendnote.Data directory (or the equivalent attachments folder), because Zotero locates file attachments relative to where the exported XML file sits, not by reading a path stored inside the file. Get that location wrong and the references import but the attached PDFs don’t.
Two real losses to expect on a Zotero import, regardless of which format you choose:
- Custom fields, author addresses, and affiliations aren’t supported EndNote-XML fields on the Zotero side — they’re converted into notes automatically tagged
_EndnoteXML importrather than dropped outright. A library with heavy custom-field use can generate enough of these notes to measurably slow Zotero down, per Zotero’s own documentation. - Formatting in RIS fields — italics, bold, anything set as in-field character formatting — does not survive an RIS-route import. If preserving that formatting matters (common in fields with foreign-language titles or emphasized terms), use the XML route instead.
Group structure isn’t addressed either way in Zotero’s own documentation — plan to rebuild your organizational structure as Zotero collections after import rather than expecting it to travel automatically.
Mendeley: fewer documented specifics, same underlying mechanics
Mendeley Reference Manager imports references via File > Import, supporting RIS among its import formats, consistent with every other major reference manager’s baseline interchange support. As with Zotero, expect the RIS route to carry references but not attachments or in-field formatting, and expect EndNote Groups to arrive flattened rather than as Mendeley folders — Mendeley’s own public documentation on EndNote-specific import behavior is thinner than Zotero’s, so treat the general RIS limitations above as the safer assumption rather than expecting file-level fidelity by default. If Mendeley Cite (its Word add-in) is the reason you’re choosing it, confirm your manuscript workflow stays in Word — it has no official Google Docs support.
JabRef: a different kind of migration, because it’s a different kind of tool
JabRef doesn’t compete with EndNote as a Word citation plugin — it manages a .bib BibTeX/BibLaTeX file for LaTeX writing, the workflow covered on CASRAI’s BibTeX file format and LaTeX bibliography styles guides. If you’re moving to JabRef, you’re very likely also moving your manuscript itself from Word into LaTeX/Overleaf, not just switching reference managers — that’s a bigger workflow change than a Zotero or Mendeley move, and worth deciding deliberately rather than as a side effect of an EndNote license lapsing. Migration mechanically follows the same RIS-export-then-import path as the other two: EndNote’s RIS output imports into JabRef as BibTeX entries, with the same reference-only, no-attachment, no-group-structure limitations described above, since RIS itself is the constraint, not any one destination tool.
What doesn’t survive any migration path
Three losses show up regardless of which of the three tools you’re moving to, because they’re properties of the RIS interchange format itself rather than of any one program’s import routine (see the RIS format guide for the field-mapping detail):
- Group/folder structure — RIS has no organizational-hierarchy concept at all; XML export can sometimes carry more, but group structure isn’t reliably preserved by any of the three destinations’ own documentation. Budget time to rebuild it.
- File attachments, via RIS — PDFs and other attached files simply don’t travel through a plain RIS file. Only an XML-style export, handled correctly, brings attachments along, and even then only Zotero’s process is well-documented enough to follow confidently.
- Some item-type and field mappings — item types without a clean 1:1 RIS equivalent (preprints, datasets, and standards are common offenders) can land in an unexpected reference type on import rather than erroring, so a post-import spot-check of anything outside a standard journal article or book is worth the ten minutes.
Before your access actually ends
If you know your EndNote access has a firm end date — a graduation date, a site-license renewal your department isn’t planning to fund, a job change — export while you still have full application access, not after. You need EndNote itself running to perform the File > Export step; once that access is gone, so is your ability to generate a fresh RIS or XML file from the live library, even though the .enl file and its paired .Data folder remain on disk. Export early, verify the import into your chosen destination while you can still cross-check against the original in EndNote, and only then treat the migration as done.
Frequently asked questions
Can I still open my EndNote library file after my license or institutional access ends?
Don’t count on it. Treat any known access end-date as a hard deadline for exporting, not as a “still have the files, will deal with it later” situation — do the export while EndNote itself is still fully usable.
Should I use RIS or XML to export from EndNote?
RIS if you only need the reference metadata and can live without attached PDFs and in-field formatting — it’s the simpler, more broadly compatible format. XML if you need attached files to come with you, particularly into Zotero, where the export-location mechanics (saving the XML into the correct attachments folder) are documented and specific enough to follow reliably.
Will my EndNote Groups become folders/collections in the new tool?
Not automatically, in any of the three destinations covered here. Rebuild the structure you actually use after import, or export group-by-group into smaller files so you at least arrive with logical chunks rather than one flat list.
Which alternative should I pick if I’m not sure yet?
Match it to how you write, not to EndNote’s feature list: Google Docs points to Zotero (the only one of the three with a native, official Google Docs plugin); staying in Word with minimal disruption points to Zotero or Mendeley; LaTeX/Overleaf points to JabRef, but expect that to mean changing how you write the manuscript itself, not just how you manage references.
