Allen helped in the planning of the attempted Spanish invasion of England, and would probably have been made Archbishop of Canterbury and Lord Chancellor if it had been successful. Allen was the head of the Roman Catholic Church in England under the Pope, and in this position, just after the death of Mary, Queen of Scots, he wrote to Philip II on 19 March 1587 to encourage him to undertake an invasion of England, stating that the Roman Catholics in England (and in Ireland) were clamouring for the King of Spain to come and punish "this woman, hated by God and man". He was made a Cardinal by Pope Sixtus V on 7 August 1587.