How to export your Mendeley library to EndNote | Library Guide


Summary

In this article, you will learn how to export your Mendeley library to EndNote.

null

Table of Contents

 

The Mendeley add-in for Word is available until 1 June 2026

The Mendeley Word add-in will be available until 1 June 2026. After that, access will be discontinued for privacy reasons. You can transfer your Mendeley references to EndNote, available via the Company Portal, Software Centre, and WUR App Store. With EndNote, you can easily insert citations and bibliographies in Word. The Library can support you during this transition.

You can join our walk-in support hours:

  • 20 April, 12:00–13:00, room B0413 (Forum)
  • 18 May, 12:00–13:00, room B0314 (Forum)

WUR Library offers the following support to get you started with EndNote

Before you get started

  • Check which version of Mendeley you are using. You are most probably using the Mendeley Reference Manager, but if you are a longtime user of Mendeley, you may still be using Mendeley Desktop. The procedure is different depending on which version you are using.
  • Depending on the complexity of your Mendeley library and what you exactly need to export to EndNote, you will need to choose between a direct export from Mendeley Reference Manager or do the export with Mendeley Desktop.
  • It is not possible to create a backup of your Mendeley Reference Manager library, so think before you click!
  • It is most likely that documents in which you have created in-text citations and reference lists will need to be manually updated unless you were using the Mendeley Cite-O-Matic tool.
  • When exporting or reattaching PDFs from Mendeley to EndNote, you will lose your annotations because Mendeley encrypts them.  

Which option should I choose when exporting my Mendeley library to EndNote?

  • I am a Mendeley Desktop user -> choose option 2
  • I am a Mendeley Reference Manager user, and
    • I have a simple library (none or a limited number of groups/collections and none or a limited number of PDFs) -> choose option 1. You will need to rebuild your library structure and reattach your PDFs manually in EndNote.
    • I have a complex library (groups/large number of PDFs) -> choose option 2. 

 

Option 1 - Simple export from Mendeley Reference Manager to EndNote

Open to see the steps

Step 1 - Export your Mendeley library

  • Open your Mendeley Reference Manager library
  • Go to File > Export All > RIS – Research Information Systems (*.ris). Important: don’t choose EndNote XML.
  • Navigate to where you want to save your export file and give it a name. Click on Save

Step 2 - Import your Mendeley library into EndNote

  • Create an EndNote library and open it.
  • Go to File > Import > File.
  • In the pop-up window that opens:
    • Import File: Choose > Navigate to where the RIS file you created from Mendeley is located and select it
    • Import Option: Reference Manager (RIS)
    • Duplicates: Import All
    • Text Translation: No Translation
  • Your references are now available in your EndNote library. We advise you to spend some time cleaning up your EndNote library (deduplications, groups, tags, etc). 

Step 3 - (optional) Adding your PDFs to your references in EndNote

With this method and due to the file structure in Mendeley, it is impossible to export PDFs along with the references. You need to manually attach them to the references. 

Our suggestion is to use the “find full text” feature in EndNote. EndNote will search the PDFs for you online and will automatically add them to your references. Note that this function works best when on campus. This means that you will only have to manually reattach PDFs to the references for which EndNote was not able to find the PDF. 

You can upload your PDFs again from the web or get them from your Mendeley library. Note that by default, Mendeley saves your PDFs in the cloud, so make sure they are available on your hard drive.

  • Go to All references > Make Available Offline.
  • Your PDF files should now be available at: C:\Users\YOUR USERNAME\AppData\Roaming\Mendeley Reference Manager\userfiles

Manually locate the files you need and attach them to your EndNote references. 

Option 2 - Export a complex Mendeley library from Mendeley desktop to EndNote

Open to see the steps

Step 1 - Open your library in Mendeley Desktop (skip this step if you are already a Mendeley desktop user)

Download the latest version of Mendeley Desktop and install it. For Windows, this will be Mendeley Desktop 1.19.8. 

Log in with your credentials and allow some time to synchronise with the entire content of your Mendeley library. 

Step 2 - Export your Mendeley library

Only PDFs are important to you; groups don't matter.
  • Make sure your PDFs are saved on your hard drive (and not just on the cloud)

As shown in the image above, PDFs uploaded to your hard drive will have the small PDF icon, while the ones still in the cloud will have the download icon with the arrow.  

  • Go to the all document tab and select all the references (Ctrl + A or Edit > select all)
  • Go to File > Export
  • Navigate to where you want to save your export file and give it a name. Select RIS – Research Information Systems (*.ris) as a "save as type". Don’t choose EndNote XML. 

Both PDFs and structure are important to you.

You will need to create an export file per group.

  • Make sure your PDFs are saved on your hard drive (and not just on the cloud)

As shown in the image above, PDFs uploaded to your hard drive will have the small PDF icon, while the ones still in the cloud will have the download icon with the arrow.  

  • Go to the group you want to export and select all the references from that group
  • Go to file > Export
  • Navigate to where you want to save your export file and give it a name. Select RIS – Research Information Systems (*.ris) as a "save as type". Don’t choose EndNote XML.
  • Repeat these steps for all your groups. Don’t forget to export the “unsorted” group as well.

Step 3 - Import your Mendeley library into EndNote

Only PDFs are important to you; groups don't matter
  • Create an EndNote library and open it.
  • Go to File > Import > File.
  • In the pop-up window that opens:
    • Import File: Choose > Navigate to where the RIS file you created from Mendeley is located and select it
    • Import Option: Reference Manager (RIS)
    • Duplicates: Import All
    • Text Translation: No Translation
  • Your references are now available in your EndNote library. We advise you to spend some time cleaning up your EndNote library (deduplications, groups, tags, etc).
Both PDFs and structure are important to you
  • Create an EndNote library and open it.
  • Go to File > Import > File.
  • In the pop-up window that opens:
    • Import File: Choose > Navigate to where the RIS files you created from Mendeley are located and select one of them.
    • Import Option: Reference Manager (RIS)
    • Duplicates: Import All
    • Text Translation: No Translation
  • Your references are now added to EndNote. Create a group and add the “imported references to it”.

  • Repeat these steps until you have added all your references and groups.
  • Your references are now available in your EndNote library. We advise you to spend some time cleaning up your EndNote library (deduplications, groups, tags, etc.). If you have references that were added to multiple groups, you will have duplicated references that you will need to remove and reorganise. 

 

Update your in-text citations and reference list in Word

If you were using Mendeley Reference Manager, there are unfortunately no automatic solutions for updating your references in a document.

You will have to go through your document manually and replace all your citations one by one with the ones in EndNote.

If you were using the Mendeley Desktop version in combination with the Mendeley Cite-O-Matic, there seems to be an option to automatically convert your Mendeley citations to EndNote. Please note that WUR Library has not tested this solution and is not providing support for this automatic conversion from in-text citations and reference lists from Mendeley to EndNote.

Delete your Mendeley account

You may want to delete your Mendeley account as well. Follow the steps as described in the Mendeley Support Center:

  1. Sign in to Mendeley.com. Click the down arrow next to your name in the top right-hand corner.
  2. Click 'Settings & Privacy'. This will open your Account page.
  3. Scroll down to the ‘Close Mendeley account’ section. Click on the ‘Close Mendeley account’ link and follow the on-screen instructions and sign out.

Please note: If you have access to other Elsevier products (such as ScienceDirect), please remember not to log in to Mendeley using your email address as this will activate the association of your Mendeley account, as Mendeley is part of Elsevier's "one login for all" policy.

Questions & support

Do you have questions about this service or, would you like personal support? Feel free to contact us.

 

Curious to find out what else WUR Library can offer you?

Visit the Library's website to access the Library’s databases and get a full overview of the Library’s services, tools, and support. You can contact a librarian anytime through the chat box on our website or click Chat online. We’re happy to help you!