As his career progressed, Bebbington moved into leadership positions within academia. He served as a Dean at both the University of Melbourne and University of Queensland. He was appointed Deputy Vice-Chancellor (University Affairs) and later Pro-Vice Chancellor of the University of Melbourne prior to his appointment as Vice Chancellor of the University of Adelaide (2012–2017). At Adelaide, he was succeeded as Vice-Chancellor by Mike Brooks in the interim, and later by Peter Rathjen, the former Vice Chancellor of the University of Tasmania and Dean of Science at the University of Melbourne.
