Later he took holy orders, held two livings, and became master of the rolls in 1494, while Henry VII.
For these and other services Bonner had been rewarded by the grant of several livings, and in 1535 he was made archdeacon of Leicester.
He was educated at St John's College, Cambridge, and successively held the livings of Islington (1662), of All-Hallows the Great, Thames Street, London (1679),(1679), and of Isleworth in Middlesex (1690).
In 1845 he entered the ministry of the Church of Scotland, and after holding several livings accepted the chair of divinity at Glasgow in 1862.
Before the end of that year he obtained from the pope a dispensation to hold two livings in conjunction with Limington, and Archbishop Deane of Canterbury also appointed him his domestic chaplain.