Between the late-twelfth and early-sixteenth centuries, much music (both liturgical and non-liturgical) was written in honour of St Thomas of Canterbury. However, in the 1530s his cult became a major target for reformers and, in 1538, Henry VIII (1491-1547) ordered the destruction of his shrine and the obliteration of all music written in his honour. This article will examine how music composed to memorialise St Thomas was treated during the Reformation and Counter-Reformation. It explores the process of self-censorship prompted by Henry’s proclamation on the cult of St Thomas that led to his erasure from liturgical books in England. It analyses the attempts by reformers to discredit music concerning St Thomas, particularly by radical reformer John Bale (1495-1563). Finally, it examines music that was composed by Catholics for St Thomas during the Counter-Reformation and asks what it can tell us about the state of the cult in the late sixteenth century. This approach results in an overview of St Thomas’ cult during the later sixteenth century and contributes to our understanding of changing conceptions of the saint by Catholic communities in the post-Reformation world.