On 7 March 1528, he was presented to the prebend of Wigginton in the collegiate church of Tamworth, but resigned it in the following July, and was appointed master of St. Bartholomew's Hospital, London.
He returned in the following year, when he and Archbishop George Browne became Henry VIII's principal instruments in introducing the Protestant Reformation into Ireland.
Staples clung to the mass, though he was strongly for the Royal Supremacy, and it was partly owing to his advice that Henry assumed the title of King of Ireland.
After Edward VI's accession, Staples's Protestant opinions became more pronounced, On 7 April 1547, he was granted the parsonage of Ardbraccan, and soon after was made judge of faculties.
He remained in his diocese, destitute and disliked, and on 16 December 1558, after Elizabeth's accession, he wrote to William Cecil relating his woes and seeking preferment.