Mendeley Reference Manager: A Replacement for Mendeley Desktop?

Last Updated on March 13, 2023

The developer once said that the Mendeley Reference Manager can replace Mendeley Desktop ​[1]​, as it is sufficient for reference management needs. Due to that, they stopped the support for Mendeley Desktop, and it is no longer available for download as of 1st September 2022. Fortunately, as you have Mendeley Desktop installed, you can still sign in and use it as usual.

Mendeley Desktop and Mendeley Reference Manager Comparison

Mendeley Reference Manager is the higher version of Mendeley Desktop. However, it seems that Mendeley Reference Manager is very different from its previous Mendeley Desktop version ​[2], [3]​.

Mendeley Desktop

• The reliable Cite-O-Matic plugin can be installed directly from Mendeley Desktop.
• Able to be used while working offline.
• A Watch Folder feature that can monitor the target folders and import new PDFs automatically to Mendeley Desktop.
• Able to import references from other software, such as Zotero and EndNote.
• Customizable citation style.
• Manual Check for duplicates feature.
• Opening Microsoft Word Cite-O-Matic in Reference is terribly slow without having to open Mendeley desktop.
• Updates are no longer available, which may lead to future compatibility issues with newer versions of MS Office.

Mendeley Reference Manager

• The Mendeley Cite plugin is only available as a download from the Microsoft Store, which may be restricted organizationally by some institutions.
• Several features (including Mendeley Cite) require the internet, making it unable to edit the references when offline.
• Minimal options and settings, making you more focused on your documents.
• Able to search for articles on the Mendeley database.
• Mendeley Reference Manager automatically checks for duplicates.
• Mendeley Cite is only compatible with Microsoft Office 365, Ms. Word 2016 and above, and Microsoft Word app for iPad.

Note that both Mendeley Desktop and Mendeley Reference Manager can use Mendeley Cite. However, Mendeley Cite is incompatible with the Cite-O-Matic, and vice versa. Even so, Mendeley Cite can convert the citations from Cite-O-Matic on a document.

Migrating to Mendeley Reference Manager

Removing Mendeley Desktop

Basically, remove the Ms. Word plugin (Cite-O-Matic) before removing Mendeley Desktop. So, several steps to remove Mendeley Desktop are as follows:

1. open Mendeley Desktop,
2. go to Tools menu > click Uninstall MS Word Plugin,
3. after MS Word Plugin has been uninstalled, go to Windows Settings > Apps > Apps & features,
4. uninstall Mendeley Desktop from your computer.

Installing Mendeley Reference Manager

Several steps to install Mendeley Reference Manager are as follows:

1. download it from Mendeley’s official website,
2. open the installer, and install it according to the instructions therein,
3. after installation, open Mendeley Reference Manager,
4. log in using your Mendeley account,
5. go to Tools menu > click Install Mendeley Cite for Microsoft Word,
   or you can directly go to Microsoft Store,
   note: you need to have a Microsoft account before downloading,
6. click Get it now and then log in using your Microsoft account when asked,
7. click the Open in Word button, and then click open link if asked,
8. Ms. Word will open and install the Mendeley Cite add-in for you.

Troubleshooting

Removing Cite-O-Matic manually

If you have uninstalled Mendeley Desktop directly, the Cite-O-Matic plugin will not be removed automatically. Hence, you need to remove it manually using the following steps:

1. open Ms. Word,
2. go to File -> Options, then select Add-Ins,
3. then in the add-ins list, click on Mendeley-x.xx.x.dotm. In this step, you will see the directory in which it is located,
4. open Windows Explorer and navigate to the folder mentioned above,
5. close all Ms. Word, if any,
6. delete the Mendeley-x.xx.x.dotm file,
7. try to reopen Ms. Word, and the plugin should no longer be loaded.

If you can’t find the mentioned folder, you may need to display hidden files and folders in settings. In the menu of Windows Explorer, click View -> Options -> Change folder and search options -> select the View tab -> Hidden files and folders -> select Show hidden files, folders, and drives.

If you use Word for Mac, the Cite-O-Matic plugin can be removed by going to Tools menu > Template and Add-Ins… > then mark Mendeley and click - ​[4]​.

Mendeley Cite couldn’t connect to the catalog

If Mendeley Cite throws an error message “We can't load this add-in because we couldn't connect to the catalog,” several steps you can try:

1. make sure that Cite-O-Matic plugin (from Mendeley Desktop) has been uninstalled from Ms. Word,
2. check your internet connection,
3. check the firewall that may block Mendeley Cite from accessing the internet,
4. if there is no issue with the internet connection, try to reinstall the Mendeley Cite,
   in Ms. Word, go to References menu > right-click the Mendeley Cite button > click Remove add-in,
   then go to Microsoft Store to reinstall the Mendeley Cite.
5. if the steps above are unable to solve the issue, change the Internet Security Zone to Medium-High ​[5]​,
   to change it, open Windows Start Menu, type internet options,
   then go to the Security tab > change the Security level for the Internet to Medium-High.

Suggestions

Both Mendeley Desktop and Mendeley Reference Manager are linked to your Mendeley account. So, using any of them may not cause any problems with your Mendeley account and its data. However, many problems have been reported in using Mendeley Cite ​[6]​, as shown in Fig 2. Therefore, you should try to experiment with it before fully using Mendeley Reference Manager. In addition, we suggest continuing to use Mendeley Desktop and not migrating to Mendeley Reference Manager until you have finished with your documents.

References