Exporting a Zotero Library into EndNote

This page covers moving references FROM Zotero INTO EndNote — the direction researchers need when an institution standardises on EndNote, a collaborator or committee requires it, or a lab’s publisher/journal workflow assumes it. (Going the other way — importing an existing EndNote library into Zotero — is a different, more commonly documented process; see Zotero’s own EndNote-import documentation if that is what you actually need.) There are two workable methods, and which one you want depends entirely on whether you need the attached PDFs to come with you.

If you have not chosen a tool yet and are deciding between the two, see Zotero vs. EndNote first. This page assumes EndNote is already the destination.

Before you start

Decide which of these you actually have, because it changes which method below you want:

• References only, no attachments — the common case when switching institutions or tools going forward; you can re-download PDFs as needed. Use the RIS method.
• References plus the PDFs already attached in Zotero — the case when Zotero is being retired entirely and this export is your only copy of the files. Use the EndNote XML method, and budget extra time for the manual file-linking step it requires.

Either way, work from a specific collection where practical rather than your entire library — Zotero lets you right-click any collection and export just that subset, which keeps the resulting EndNote library from arriving as one undifferentiated pile of references with no folder structure. Zotero’s nested collections do not carry over as EndNote Groups automatically on import; whatever organisation you want on the EndNote side, plan to rebuild it there (or export collection-by-collection into separate EndNote libraries, then combine).

Method 1 — Export as RIS (references only, the default choice)

RIS is the older, simpler interchange format both programs read and write, and it is the right default when attachments are not the point.

1. In Zotero, select your library or the collection you want to move, then use the gear icon (or right-click the collection) and choose Export Library / Export Collection.
2. Set the format to RIS. Leave “Export Files” unchecked — checking it does not make the PDFs travel through an RIS file (RIS is a plain-text reference format with no file-attachment mechanism); it only adds bulk you do not need for this method.
3. Save the resulting .ris file.
4. In EndNote, open the target library and go to File > Import > File. Choose the .ris file, and set the import filter to Reference Manager (RIS).
5. Run the import, then spot-check a handful of records — particularly any conference papers, book chapters, or web pages, which are the item types most likely to land in the wrong EndNote reference type (see below).

Method 2 — Export as EndNote XML (keeps PDF attachments)

Zotero can export directly in an EndNote-native XML format, and — unlike RIS — this path can carry the attached files along, at the cost of one extra manual step.

1. In Zotero, select the library or collection, open Export Library / Export Collection, and set the format to EndNote XML.
2. This time, check “Export Files.” Zotero writes the .xml file plus a separate folder containing the attached PDFs.
3. In EndNote, File > Import > File, choose the .xml file.
4. The attachments do not link themselves. After the import, you have to manually copy the contents of Zotero’s exported PDF folder into the new EndNote library’s own .Data folder (the same hidden data folder that stores everything else attached to that .enl library) so EndNote can find and relink the files to the correct records. This is a real, easy-to-skip step — importing the XML alone gives you correct reference records with no PDFs attached.
5. Spot-check several records with attachments afterward to confirm the PDFs actually relinked, before you consider the migration done and delete anything from Zotero.

What the RIS method loses in translation

This is the part worth planning for, not discovering after the fact. RIS is a fixed, decades-old tag format (a “TY” type code on the first line, then tagged fields like AU for author or TI for title) that was never designed around either program’s specific item-type list, and Zotero and EndNote do not define exactly the same set of reference types. A Zotero item type without a clean RIS equivalent — preprints, blog posts, podcasts, and standards are the common offenders — gets coerced into whatever generic RIS type is the closest fit, and can land in an unexpected EndNote reference type after import rather than failing outright, which is why spot-checking matters more than trusting a “0 errors” import summary.

Other things RIS strips or can mangle in the round trip: any rich-text formatting inside a field (italics or bold in a title or abstract does not survive), Zotero’s freeform Extra field and item-to-item Related links (RIS has no equivalent field for either), and — inconsistently, by item type — some structured fields like edition or a multi-volume work’s volume count, per longstanding user reports in Zotero’s own support forum. None of this is a bug in either program; it is RIS being a narrower format than either tool’s native data model. For the mechanics of why two RIS exports of the “same” data can differ, see The RIS File Format: Tag Reference, Why Exports Differ, and How to Repair One by Hand.

The EndNote XML method (Method 2) avoids most of this, since it is a richer, EndNote-native format rather than a lowest-common-denominator interchange one — another reason to prefer it when the migration is a one-time, permanent move rather than a routine sync.

After the import: checking your library

Before treating the migration as finished:

• Spot-check reference types across a sample of items, not just a count of imported records — a clean import summary does not mean every item landed in the right EndNote type (see above).
• If you are importing into a library that already has records — rather than a brand-new empty one — run EndNote’s duplicate check afterward rather than assuming the import caught overlaps with what was already there.
• For Method 2, confirm PDFs actually opened from inside EndNote (not just that files exist in the .Data folder) on a few records before deleting your Zotero copy.
• Keep the original Zotero library intact until you have verified the EndNote library independently — treat this as a copy operation, not a move, until you are certain nothing was lost.

For the reverse workflow — building out a new EndNote library from scratch rather than migrating one in — see How to Use EndNote: A Researcher’s First-Project Walkthrough. If you are instead exploring whether to leave EndNote for Zotero, or want the general Zotero setup path, see Zotero for Researchers and Zotero Setup and Troubleshooting.

Frequently asked questions

Do I need to uninstall Zotero once EndNote has the library? No — nothing about this migration requires it, and keeping Zotero installed with the original library intact is the safest way to confirm the EndNote copy is complete before you rely on it.

Can I go back to Zotero later if EndNote does not work out? Yes; EndNote libraries can be exported and re-imported into Zotero using the same interchange formats in reverse, though you would want to expect the same category of field-mapping losses on the way back.

Which method should I use if I am not sure whether I need the PDFs? Default to the EndNote XML method (Method 2) if there is any real chance you will retire Zotero afterward — it is more work up front, but the RIS method genuinely cannot carry attachments at all, and re-downloading a large PDF collection later is far more painful than one extra file-copy step now.