At length, on the death of John Munckley (August 1738), he was strongly recommended by Benjamin Avery as a suitable candidate for the charge of the presbyterian congregation at Bartholomew Close. There, Fleming and William May were ordained as joint pastors in 1740. Fleming had scruples about presbyterian forms, and classed himself as an independent. At his ordination, conducted by Samuel Chandler, D.D., Jeremiah Hunt, D.D., a learned independent, and others, he refused to submit to the imposition of hands, His confession of faith was unique. He would only say that he believed the New Testament contained 'a revelation worthy of God to give and of man to receive;' and this he promised to teach in the sense in which he should 'from time to time' understand it. It was soon rumoured that Fleming was a Socinian. His congregation was never large, and the scantiness of his stipend reduced him to dire financial straits. His friends fell off, with the exception of Jeremiah Hunt. After Hunt's death (1744) Fleming contracted an intimacy with Nathaniel Lardner, D.D., his neighbour in Hoxton Square, and co-operated with him in literary work. In January 1752 James Foster, became disabled from preaching. John Weatherley (d. May 1752), a General Baptist minister, who supplied Foster's place, met Fleming at Hamlin's Coffee-house, and engaged him for a Sunday at Pinners' Hall, an Independent congregation. He attracted the notice of Timothy Hollis, was soon afterwards elected as Foster's assistant, and on Foster's death (5 November 1753) as pastor. The Bartholomew Close congregation then came to an end, its few remaining members joining Pinners' Hall. For nearly a quarter of a century Fleming remained at his post; his ministry, though painstaking, was not popular, and when he ceased to preach, in December 1777, his congregation became extinct, the lease of their meeting-house expiring in 1778. He had admirers, who left him considerable legacies, among them being a bequest by a Suffolk gentleman (Reynolds), who had once heard him preach but did not know his name. A wealthy widow placed her whole fortune at his disposal. Fleming, however, declined to be enriched at the expense of her needy relatives. In his old age his friend William Dalrymple of Ayr procured for him the degree of D.D. from St. Andrews. Fleming was inclined to reject this 'compliment;’ but his friend Thomas Hollis 'put it into the public papers,’ so Fleming accepted