Fortescue, who was throughout his life a zealous Roman Catholic, for several years harboured at Cookhill the Benedictine monk, Augustine Baker.
In 1605, after the Gunpowder Plot and the rising of the Roman Catholics of Warwickshire, Fortescue underwent several examinations, and fell under some suspicion on account of a large quantity of armour found in his house.
A letter from Chief-justice Anderson and Sheriff Warburton to the Privy council states that Fortescue of Warwickshire, though summoned to appear before them, had not come forward to be examined.
He succeeded in clearing himself from these suspicions and lived at Cookhill unmolested until about 1610, when he was appointed a commissioner of James's household and of the navy.
He was knighted in 1618, and in the same year, on the death of Sir John Poyntz (formerly Morice) of Chipping Ongar, he obtained the lucrative and honourable post of Chamberlain of the Exchequer, which he held until May 1625, when he resigned it.