In recent years, JGU has established modularized Bachelor's and Master's degree programs in all subjects, with the exception of those regulated by nationwide standards (Law, Human Medicine, Pharmaceutical Sciences) and the Fine Arts. In addition, a wide range of doctoral programs is offered.

JGU is the first German university to have successfully undertaken the "system accreditation" procedure, and since March 2011 has had the right to independently (re-)accredit its own degree programs.

Currently, 106 Bachelor's and 116 Master's degree programs are available, as well as approximately 200 subject combinations for college preparatory secondary school teacher training (B.Ed. and M.Ed.). In order to avoid overlap within these subject combinations, JGU has introduced a so-called "time-frame model" based on outside expertise.

This broadly diversified and attractive range of courses, which reflects JGU's status as a comprehensive university, uses three different degree program models. In addition to single or dual subject degree programs, opportunities have been made available particularly for former Magister degree programs to not only retain their specific fields of subjects, but to extend these at the interface of various academic disciplines. This initiative is supported by numerous interdisciplinary courses and courses that transcend faculty cultures, such as those offered by the university’s General Studies program on questions of the intercultural and interdisciplinary aspects of teaching science and methods.

Alumni surveys of recent years have shown that JGU students quickly manage the transition into professional life after having taken their final exams, highlighting the practical orientation and close professional confluence of the teaching.