Duffy moved to Magdalene College in the University of Cambridge in 1979, and was professor of the history of Christianity from 2003 to 2014. Since 2014 he has beenemeritus professor.[9] In 2004 he was elected as a fellow of theBritish Academy.[10]
Longman–History Today Award for book of the year (1994):The Stripping of the Altars: Traditional Religion in England 1400–1580[11]
Hawthornden Prize for Literature (2002):The Voices of Morebath: Reformation and Rebellion in an English Village[12]
Honorary fellow,St Mary's College, Twickenham (2003). (He later resigned from the position in protest of management decisions at the college made by its principal,Philip Esler)[13]
Humanism, Reform and the Reformation: The Career of Bishop John Fisher (1989; transferred to digitally printed hardback and paperback in 2008) (Editor; co-edited with Brendan Bradshaw)ISBN0521340349 (1989)ISBN978-0-521-34034-2 (2008, hardback)ISBN978-0-521-09966-0 (2008, paperback)
"The Shock of Change: Continuity and Discontinuity in the Elizabethan Church of England", inAnglicanism and the Western Catholic Tradition (2003, edited byStephen Platten)ISBN1853115592
Saints, Sacrilege and Sedition: Religion and Conflict in the Tudor Reformations (2012; transferred to paperback in 2014)ISBN1441181172 (2012)ISBN9781472909176 (2014)
Reformation Divided: Catholics, Protestants, and the Conversion of England (2017)ISBN9781472934369
Royal Books and Holy Bones: Essays in Medieval Christianity (2018)ISBN9781472953230