“System accreditation” is a new approach developed for German universities to conduct the mandatory accreditation of all their study programmes. A pilot project at Johannes Gutenberg University in Mainz is playing an important role in paving the way for this alternative to prevailing programme accreditation. This article describes how system accreditation, an innovative approach towards organisational adaption to national regulations, was conceived and how it functions. Based on the experience of Johannes Gutenberg University, the article explores the potential of system accreditation to improve quality assurance and the development of study programmes. System accreditation faces three global challenges: that of creating an integrated approach, establishing a solid evidence base and fostering the effectiveness of evaluation efforts.