He was brought up a Roman Catholic. He had fought on the Spanish side in the Netherlands under Alva from 1567 to 1570, and then served the English crown in Ireland. Throughout the period of his service in Ireland, he had fought with distinction, despite being a co-religionist of his anatgonists. When in 1585 he was sent to the Netherlands, his loyalty to the crown was on the one hand apparently unquestioned, but on the other there had been rumours of links with Jesuit priests and connections with the Babington plot. With hindsight, therefore, it was a mistake to to have put him in command of the recently acquired city of Deventer with an army of Irish Roman Catholics. Despite Leicester having defended his loyalty to the suspicious Dutch, Stanley betrayed the town to the Spanish, the day after Zutphen had similarly been betrayed by the English commander Rowland York (January 28th).
Shortly after the event, Cardinal William Allen wrote a pamphlet defending Stanley's actions with a view to justifying the assassination of Elizabeth I as provided for in the bull Regnans in Excelsis.