Upon Perrot's return to England he was elected Member of Parliament in 1589 for Haverfordwest and appointed to the Privy Council, where he maintained his interest in Irish affairs through correspondence with several members of the council in Dublin. However his enemies were working against him. In the heated politics following the defeat of the Spanish Armada he was accused of treason, based on allegations made in Ireland by a former priest and condemned prisoner, Sir Dennis O'Roghan. The evidence was provided in letters allegedly addressed by Perrot as Lord Deputy (with his signature attached) to King Philip II of Spain and the Duke of Parma, in which certain treasonable promises were made on the future dominion of England, Wales and Ireland.