The Moses Mendelssohn Center for European-Jewish Studies (MMZ) was founded in 1992 - the 50th anniversary of the infamous Wannsee Conference and the 500th year of the expulsion of the Jews from Spain. With the support of the Brandenburg state government, the MMZ was established as an affiliated institute of the University of Potsdam, conducting interdisciplinary research on European-Jewish history and its present, while at the same time contributing its own topics to academic teaching. The MMZ was thus instrumental in the conception and development of the course of study "Jewish Studies", which opened at the University of Potsdam in the winter semester of 1994/1995.

With substantial support from the MMZ, an academic partner institution in Saxony-Anhalt, the Moses Mendelssohn Academy (MMA) in Halberstadt, was founded in 1995. In the rooms of the former rabbinical seminary there, a meeting place for the promotion of tolerance and intercultural communication - with accompanying educational programs - was established next to the Berend-Lehmann-Museum.

In 1996, the Moses Mendelssohn Center moved to its new home at Neuer Markt in Potsdam's historic center, thus becoming part of the "Forum Neuer Markt" association of humanities and social science institutions. The steady growth of the library of the MMZ, the establishment of graduate programs and the increasing number of public events led to the MMZ frequently attracting not only scholars, lecturers and students but also educators, journalists, politicians and generally interested citizens of Potsdam. In May 2007, the MMZ was named a "Landmark in the Land of Ideas". The "Library of Burned Books" project was selected as part of the "Land of Ideas" location initiative under the patronage of the then Federal President Horst Köhler.

In recent years, the MMZ has, on the one hand, strengthened the international connections of its own research and, on the other hand, has increasingly emphasized the broadest possible dissemination of scholarly findings on Jewish history and the present. In addition to a large number of publications, traveling exhibitions on the trial of Alfred Dreyfus, the work of Theodor Herzl and Israeli society today, the history of the Jewish Hospital in Berlin, the philosopher and publicist Theodor Lessing, the Prussian Emancipation Edict of 1812, and the history of all the synagogues in what is now the state of Brandenburg, among others, all served the latter purpose.

Since the beginning of the new millennium, cooperations with partner institutions abroad - especially in the USA and Israel - have been expanded and strengthened. In cooperation with Brandeis University (Waltham, Massachusetts), Augusta State University (Georgia)  and Tel Aviv University, among others, studies on transnational Jewish migration after 1989 and on the development of European Jewry after the end of the Cold War were initiated.

Since 2010, the MMZ has been intensively involved in the establishment of the Center for Jewish Studies Berlin-Brandenburg (ZJS), a network funded by the Federal Ministry of Education and Research and inaugurated in 2012, which also includes the Free University of Berlin (Jewish Studies), the Humboldt University of Berlin (Cultural Studies), the Technical University of Berlin (Center for Research on Antisemitism), the University of Potsdam (Jewish Studies), and the Abraham Geiger Kolleg (AGK). The ZJS promotes synergy effects between the above-mentioned institutions and enables joint profiling in terms of content.

With support from the Friedrich Naumann Foundation for Freedom (FNF), the Walther Rathenau Kolleg "Liberalism and Democracy" was established at the MMZ in May  2010. Another graduate college, the Ludwig Rosenberg Kolleg, began its work at the MMZ in summer 2013 with the support of the Hans Böckler Foundation. Here, doctoral students conduct research on selected topics in the field of "The Labor Movement and Judaism.