In 1678 he succeeded Gale, both as pastor of the independent church in Holborn and as tutor in the academy at Newington Green.
He moved his congregation to a meeting-house at Girdlers' Hall, Basinghall Street, and took his academy successively to Clapham and, about 1687, to Little Britain.
His ministry was successful; but it was as a tutor, especially in philosophy, that he made his mark as an early adopter of new ideas.
He was the first to desert the traditional textbooks, introducing his pupils, about 1680, to what was known as ‘free philosophy.’ Rowe was a Cartesian at a time when the Aristotelian philosophy was still dominant in the older schools of learning; but while in physics he adhered to Descartes against the rising influence of Isaac Newton, he also became one of the earliest exponents of John Locke.
He succeeded Stephen Lobb in 1699 as pastor of the independent church in Fetter Lane.