Prof. Mendes-Flohr has written some thirty books, edited another forty-five, and authored some 300 articles. In addition, in 2019, after twenty years’ work—with Peter Schaefer (until 2010) and Bernard Vitta (subsequently)—he completed a critical edition of the collected works of Martin Buber (21 volumes containing 26 books, in German). This edition, Martin Buber Werkausgabe, was under the auspices of the Israel Academy of Sciences and Humanities (of which Buber was the founding president), the Berlin-Brandenburg Academy of Sciences and Humanities, and the Heinrich Heine University in Düsseldorf.

Between 1990 and 2006 Prof. Mendes-Flohr was the director of the Franz Rosenzweig Minerva Research Center, at the Hebrew University of Jerusalem. He is professor emeritus at the Hebrew University of Jerusalem and the University of Chicago and a member of the American Academy of Arts and Sciences.