This article examines the development of Protestant thought in early Elizabethan England by analysing James Pilkington's 1560 commentary on the Old Testament book of Aggeus (Haggai). Pilkington's commentary contained ideas about the Church and its reform that had deep affinities with radical Marian Protestant thought about purity, separation and resistance to ungodly monarchs. The way in which Pilkington transformed these ideas in a time of Protestant political ascendancy provides valuable insights into the nature and development of English Puritanism.