He was appointed, in 1691, lecturer of St Mary Hill, London, and on 16 June 1695 he became preacher of Highgate Chapel, where he had already been officiating for some time previously, during the illness of his predecessor.
Before this, he had been appointed one of the six chaplains to Princess Anne of Denmark at Whitehall and St James's, a position which he continued to hold after she came to the throne, and during part of the reign of George I.
On coming to live at Highgate, seeing the lack of affordable medical advice, he applied himself to the study of medicine, and used his knowledge for the free care of his parishioners.
The archdeaconry of Rochester becoming vacant by the death of Thomas Sprat (1679–1720), Atterbury wrote to his younger brother, the bishop, applying for the post.
At the age of seventy, up to which time he had enjoyed good health, he suffered an attack of the palsy and began to pay frequent visits to Bath, Somerset.