From 1987 to 1991 he worked as an academic assistant at the Institute of Statistics and Mathematical Economics of the University of Karlsruhe where he finished his Ph.D. in the year 1990 with a thesis on individual decision theory under risk.

A key encounter for his future academic career was with Amartya Sen who introduced him to the problem of the measurement of freedom.

After his return to Europe, Clemens Puppe worked from 1993 to 1997 as assistant professor at the Fakultät für Wirtschaftswissenschaften der Universität Wien [de] of the University of Vienna, where he submitted his `Habilitation´ in the year 1997.

Following articles on the measurement of freedom of choice[2][3] Clemens Puppe published in collaboration with Klaus Nehring papers on diversity theory,[4] judgement aggregation[5] and non-manipulable voting rules,[6] among others.

He also worked in the area personnel economics in collaboration with Michel Maréchal und Sebastian Kube.