In November 1684 Manningham was made preacher at the Rolls Chapel, and from about 1689 to 1692 was head-master of Westerham grammar school, Kent.
He subsequently became rector of St. Andrew, Holborn, on 8 September 1691; chaplain in ordinary to William III and Mary II; canon at St George's Chapel, Windsor on 28 January 1692-3 (until 1709); rector of Great Haseley, Oxfordshire, 1708; and dean of Windsor on 26 February 1709.
Manningham printed many sermons between 1680 and his death, and was author of Two Discourses, London, 1681, and The Value of Church and College Leases consider'd in Sir Isaac Newton's Tables, 1742.
(d. 1750), treasurer of Chichester in 1712, prebendary of Westminster in 1720, and rector of Slinfold and Selsey, Sussex; Sir Richard Manningham, M.D.
; and Simon Manningham, prebendary of Chichester (1719–67) and vicar of Eastbourne (1720–34); and two married daughters, Mary Rawlinson and Dorothea Walters, besides five other children.