[1] Fowler was suspected of Pelagian tendencies, and his earliest book was a Free Discourse in defence of The Practices of Certain Moderate Divines called Latitudinarians (1670).
It also took aim at Thomas Hobbes, by means of positions set out by Daniel Scargill, an apostate Hobbist.
Bunyan described the Design as "a mixture of Popery, Socinianism and Quakerism," an accusation to which Fowler replied in a scurrilous pamphlet entitled Dirt Wip'd Off.
He also published, in 1693, Twenty-Eight Propositions, by which the Doctrine of the Trinity is endeavoured to be explained, challenging with some success the Socinian position.
He was successively rector of St. Mary the Virgin's Church, Northill, Bedfordshire (1656) and of All Hallows, Bread Street, London (1673), and in 1676 was elected a canon of Gloucester; his friend, Henry More, one of the Cambridge Platonists, resigned in his favour.