Breton was admitted to the College in 1629. He was elected Master by royal mandate in 1665, following the resignation of William Sancroft on his appointment as Dean of St. Paul’s.
He was a high churchman, and no doubt for this reason had not been elected to a fellowship during the Commonwealth period. His first order as Master was for the closure of the College because of an outbreak of plague in Cambridge, and a further outbreak in the summer of 1666 closed it again. The number of students in the college in his time increased to an average of 40. The building of the Wren chapel was begun while he was Master, and in 1668 he went to Northamptonshire to sign a contract for the supply of stone.
He was buried in the old chapel and his body was removed to the new chapel after its completion; a grave believed to be his was discovered during the restoration of the chapel in 2004.