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Mendeley: Mendeley FAQs

A how-to manual for the reference management tool, Mendeley

Mendeley FAQs


  • Migrating from Mendeley Desktop to Mendeley Reference Manager
  • What is the difference between Mendeley Desktop and Mendeley Reference Manager?
  • Notable differences between Mendeley Desktop and Mendeley Reference Manager
  • Creating a Mendeley Account



Migrating from Mendeley Desktop to Mendeley Reference Manager

Migrating your library should not cause you any issues since both Mendeley Desktop and Mendeley Reference Manager are synchronised with your Mendeley account. However, the new in-text citation tool, Mendeley Cite works with a different MS Word function than the original Cite-O-Matic. Although it is possible to convert citations from the Cite-O-Matic tool to Mendeley Cite, it can still have issues and several users have experienced problems in attempting the conversion.

Therefore, if you are currently busy with a manuscript and you have been using Mendeley Desktop, we strongly recommend that you do not migrate to Mendeley Reference Manager until you have finished with your current research.

What is the difference between Mendeley Desktop and Mendeley Reference Manager?

Both Mendeley Desktop and Mendeley Reference Manager are downloadable applications that are used for bibliographic reference management. Mendeley Desktop is the original version that allowed you to work seamlessly even if you are working offline. Mendeley Desktop’s Cite-O-Matic plugin for MS Word simplifies in-text citations and reference management. Mendeley Reference Manager is the newer version and it will eventually replace Mendeley Desktop.

Notable differences between Mendeley Desktop and Mendeley Reference Manager

Mendeley Desktop (MD)

  • Multiple ways to import references
  • You can import references from other reference managers
  • You can create a Watch Folder. If you store a PDF document in the Watch Folder, its metadata will automatically be uploaded to Mendeley Desktop and it will create a record
  • You can export PDF documents with the annotations you have made to it
  • Easy access to the style customisation platform
  • You can manually check for duplicates and select the most accurate version
  • The Cite-O-Matic is a stable and reliable MS Word Plugin and allows for greater customisations of citations and their fonts
  • Easier to use while working offline

Mendeley Reference Manager (MRM)

  • Mendeley Reference Manager does not have any of the above features
    • An exception is the option to import references from other reference managers, however the feature is frustrating and not easy to use
    • MRM automatically checks for duplicates, but it is not very efficient
  • MRM has a Notebook feature that collates all the notes you make in your various references
  • Easier access to searching for articles on the Mendeley database
  • Mendeley Cite (MRM's MS Word plugin)
    • The new MS Word plugin allows you to browse your Mendeley library in MS Word
    • You can change the referencing style
    • Automatically synchronises with MRM

Creating a Mendeley Account

When creating a Mendeley account, it is very important that you do not use the “Sign in via your institution” option, as SU does not have this integration with Mendeley. Instead, please follow these steps:

On the Mendeley homepage, select Create Account:

When prompted, enter your email address (it can be your personal or email address) and click continue:

When prompted to create a password, do not use the same password that you use for your SU accounts, as this may prevent you from logging in to the desktop applications.

Once you have filled in all the required information, you can start using Mendeley.


  • Common issues
  • Installing Mendeley Desktop on Mac devices
  • Installing custom styles in Mendeley Desktop



Common Issues

Since Mendeley Desktop is an older version of the reference management software, it may have some future compatibility issues with MS Office 365.

  • If the Cite-O-Matic plugin is missing in the References tab, you can follow these steps to fix the issue:
    • Step 1: Open Word, then go to "file"->"options", a new window pops out.
    • Step 2: Select "Add-ins" in the left, then select "word add-ins" in "manage" (at the bottom), and click on "Go"
    • Step 3: Click "add", then select "Mendeley 1.19.4.dotm" from the Mendeley installation file, it may be in "C:\Program Files (x86)\Mendeley Desktop\wordPlugin"
    • Step 4: Click OK, then you should find mendeley in the "reference" tag on the top of word 365.
      • Credit: Huang, W. 2019. How to add Mendeley plugin into word. [Online]. ResearchGate. Available: [2022, July 15].
  • If the above solution does not work, please contact Kirchner van Deventer or Letlao Seloma for assistance.

A reference saved in Mendeley Web does not appear on Mendeley Desktop

  • In Mendeley Desktop, click on the "Sync" button in the toolbar

Some of my references have missing or incorrect information

  • Mendeley reference managing software only picks up the available data that it receives in .RIS or other file types. The information, or metadata, is often incomplete or incorrect. It is, therefore, very important that users double check each reference to make sure that the information is accurate and complete.

Mendeley Desktop can't connect to the internet

When you encounter this error message, it's usually indicative of one of two problems that are preventing Mendeley Desktop from contacting the Mendeley Web servers.

  1. A temporary issue either on our servers, or with your ISP routing to our servers, is preventing a connection. Check that you can access within your web browser to verify if this is the case.
  2. Local settings are blocking Mendeley Desktop from connecting out. This may be due to firewalls, or anti-virus software on your computer, or further down in your network setup (especially if you're on a public computer/network).

If you have admin rights try either disabling the firewall/anti-virus temporarily, or add an exception that explicitly allows Mendeley Desktop connectivity. You may require proxy settings for Mendeley Desktop to connect. These settings vary from location to location and you'll need to consult whomever maintains your network for this information. Once proxy setting are acquired, you can either set this up (or disable it if not needed) within Mendeley Desktop by going to Tools > Options > Connection. Check with your administrator about your proxy settings, it may be that your problems are caused by security software on your network that is blocking Mendeley Desktop. If you're on a private network, you should be able to configure this yourself.

Installing Mendeley Desktop on Mac devices

If you encounter this message on your Mac device, you can fix the issue with the following steps:

Go to Settings and select Privacy & Security:

Go to the General tab at the top and click on "Open Anyway"

Installing custom styles in Mendeley Desktop

Step 1: In the toolbar select View and click on Citation Style:

Step 2: Click on More Styles...

Step 3: In the Citation Styles tabs select Get More Styles

Step 4: In the search bar, search for Stellenbosch > Select Stellenbosch University Harvard and click on Install

If you want to install a style using a URL:

Step 1: Follow above steps 1 to 3

Step 2: In Get More Styles paste the URL in the Download Style bar at the bottom of the window and click on Download:



  • Common issues
    • Mendeley duplicates my in-text citations
    • Mendeley Cite Add-In Warning
    • Mendeley Cite is not appearing in the 'References' tab in MS Word
  • Mendeley Reference Manager: Known issues when working offline

Common Issues

Mendeley duplicates my in-text citations

If Mendeley creates duplicate in-text citations whenever you insert a citation, it is most likely because you have track changes enabled. Unfortunately, Mendeley is currently incompatible with MS Word's track changes function and it will continue to create duplicates as long as track changes is enabled. Mendeley is working with Microsoft on a solution, but there is no indication on when this problem will be fixed.

Mendeley Cite Add-In Warning

If you encounter the following error while trying to run Mendeley Cite, it is because you are using an older version of MS Word (2016 or older) and the latest version of Cite is not compatible yet.

Mendeley Cite is not appearing in the 'References' tab in MS Word

Users who are using Microsoft Word 2016 will notice that after installing Mendeley Cite, the add-in will disappear from the 'References' tab once Microsoft Word is closed and reopened. This is because Microsoft Word 2016 does not support add-ins that were downloaded from Microsoft AppSource to remain within the ribbon tabs in Microsoft Word after it is closed, and the add-in will disappear from the ribbon. Microsoft have stated that they will not be implementing a fix for this.

To access Mendeley Cite after you have installed it in Word 2016, you will need to access it through the add-ins menu. To do this, click on the 'Insert' tab and select the 'My Add-ins' option. Here you should see a menu load which contains Mendeley Cite.

Mendeley Reference Manager: Known issues when working offline

There are some aspects of functionality in Mendeley Reference Manager that are not yet available offline; these are listed below. Check back for details of when this will be available.

Importing references via methods other than creating a manual entry are not available while offline.

Copying references with file attachments between your private library and different groups and then amending the file attachments from either the new references or the original will not sync correctly when going online. New references will mirror the original reference at the point of going online and any file amendments will be lost.

Creating both a collection and a manually added reference while offline, and then moving the new reference to the new collection without going online will cause the new reference to become corrupted.

When using the features within the group management functionality you will notice that some options are disabled, this is to prevent any issues occurring for other members in the group.

Managing which documents are stored for offline use whilst on the web version of Mendeley Reference Manager.

If the answer you are looking for is not in our compilation of FAQs, please have a look at the following Mendeley Resources: