Mendeley has been working with a wide range of universities:
- University of Alberta
- University of Arkansas at Fort Smith - Boreham Library
- Blekinge Institute of Technology
- University of British Columbia
- University of California, San Diego
- University of California, San Francisco - UCSF Library
- University of California, Irvine
- University of Cambridge - University Library
- University of Cambridge - Balfour & Newton Libraries
- University of Cambridge - Science Portal
- Canadian Federation for the Humanities and Social Sciences
- Technische Universität Chemnitz
- Centrale Lyon - Bibliothèque Michel Serres
- Centre College Danville, Kentucky
- University of Colorado at Boulder
- Columbia University
- Columbia University - Augustus C. Long Health Sciences Library
- University of Copenhagen
- University College Cork
- Cornell University
- University of Cyprus
- Dartmouth College
- University of Denver - Westminster Law Library
- University College Dublin - Geary Institute
- Duke University
- Fred Hutchinson Cancer Research Center
- George Mason University
- Georgia Tech
- Goethe-Universität - Frankfurt am Main
- University of Groningen
- Johns Hopkins University - Sheridan Libraries
- Harvard University
- University of Hawai'i
- Heriot-Watt University Edinburgh
- University of Illinois at Urbana-Champaign
- Imperial College London
- IONA College, New Rochelle
- Joint Information System Committee
- University of Illinois at Springfield
- Kutztown University
- Lancaster University
- University of Leicester
- University Leiden
- University of Manitoba
- Mary Baldwin College
- Marymount University
- Massachusetts Institute of Technology Libraries
- McKay School of Education
- University of Michigan
- University of Minnesota
- MIT - Massachusetts Institute of Technology
- Montana State University
- New York University
- University of Nevada, Reno
- NHS Trust - North West Ambulance Service
- North Carolina State University
- University of Nottingham
- Ohio State University
- Oregon State University
- Pacific Lutheran University
- Purdue University - Biometric Standards, Performance & Assurance Laboratory
- Penn State University
- Princeton University
- The University of Queensland Australia
- Radcliffe Science Library
- Research Information Network
- Rice University
- San Diego State University
- The Serbian Academy of Sciences and Arts
- University of Sheffield
- Stanford University - School of Medicine
- Stanford University - Social Science Research Center
- Swansea University
- Syracuse University
- Universita di Torino
- Trinity College - Graduate Studies
- Eberhard Karls Universität Tübingen
- UK PubMed Central
- University of Vermont
- Washington and Lee University Library
- Washington University in St. Louis
- Weill Cornell Medical School
- The Welsh Repository Network
- University of Wisconsin, Madison
- Zürcher Hochschule der Künste