Custom tools to export your EndNote library to Zotero

Samuel Mok published on
5 min, 837 words

Categories: Reference Managers Zotero EndNote

Tags: references guides

If you want to export your current EndNote library to Zotero, you should use the .xml export function of EndNote as explained in the official Zotero docs. There are a few problems that can crop up when doing this: commonly users experience difficulty with transfering their .pdf files for example, and this export/import will also overwrite the added to / last changes dates of all items. While the Zotero docs explain how to solve the issue with the .pdf files, there is no easy solution to the issue with the dates. Therefore I developed a small program to export your EndNote library that properly includes the required information, combined with a small Zotero plugin that can set the added to / last change dates back to the original EndNote-based dates. Along the way I also added some extra functionality to retrieve more fields than the default Endnote export, and this will also allow full library exports when your Endnote license expires.

The full instructions can be found below. The guide & application are meant for Windows. If you want to run it on e.g. MacOS you'll need to make a few changes to the source code of the export tool, which you can find here: endnote-exporter. The source code for the Zotero plugin is available here: endnote-date-fixer

Download the latest exporter & plugin here:

Instructions for the custom Endnote Exporter

by Samuel Mok / [email protected] / samuelmok.cc

january 2026

for endnote exporter v1.3, windows specific instructions

source code, dev details, download for other platforms: https://github.com/utsmok/endnote-exporter

source for accompanying zotero plugin: https://github.com/utsmok/endnote-date-fixer

I. Transferring your Endnote library to Zotero

A. Download & start the endnote exporter

  1. Download Endnote Exporter
  2. Go to your downloads folder, then right click on endnote_exporter_v1.3, and click Properties.
  3. Click the checkbox next to 'Unblock', then press Apply and OK.
  4. Launch the exporter by double clicking on endnote_exporter_v1.3.

B. Use the endnote exporter to create an .xml from your Endnote library

  1. Press Select .enl file.

  2. It should open the directory with your Endnote library file(s) if you used the default directories. Select the library you want to export and hit OK.

    2a. Don't see any library files on your screen? Then you will need to navigate to the correct folder yourself. Once you open the correct directory, you should see you library file(s) appear, as the file selector will only show files of the correct type.

  3. Now you can press the Export to XML button. Choose where to store this file. TIP: Pick an easy to find location, for example your downloads folder or desktop.

  4. The app will let you know if it was successful, and show an error message if it failed.

    4a. Got an error? Read the error message and/or the .log file in your downloads folder with some more details (endnote_exporter.log) to see if you can fix it yourself.

    4b. Don't know how to solve? Get in touch with me ([email protected]), let me know the issue. Ensure you send along the debug file and the error message with your help request so I know what went wrong according with the export.

C. Importing the .xml file into Zotero

  1. Start up Zotero.
  2. Press File → Import
  3. Press Next
  4. Select the .xml file you saved in step B.
  5. Press Next and wait for Zotero to finish. This can take a while for large imports, especially if you stored a lot of PDFs.
  6. Close the wizard, and you should see all your items in Zotero now.

II. Endnote import metadata fixer

If you want to clean up the metadata for the imported items so they have the same creation & modified dates as they had in Endnote, plus clean up some additional fields, you can use the accompanying Zotero plugin endnote-date-fixer.

A. Download & install the plugin

  1. Download the plugin here. If you're using Firefox, make sure to use right click → save as... on this link, otherwise it will try to open the file as a Firefox plugin.
  2. Open Zotero
  3. Open Tools → Plugin
  4. Press the 'gear' icon in the top right and select Install plugin from file.
  5. Navigate to your download dir and select endnote-date-fixer.
  6. Press 'Yes' and/or 'OK' on the following dialogues until the plugin is installed.

B. Use the plugin

  1. Open Zotero
  2. Ensure you imported your Endnote library using the endnote exporter as outlined above in section I
  3. Open Tools → Fix Endnote Import Dates
  4. This can take quite a while. It will run steadily in the background as long as you do not close Zotero. You can do something else in the meantime!