Goodwin was born in Norfolk and educated at Queens' College, Cambridge, where he graduated M.A. and obtained a fellowship on 10 November 1617. He left the university and married, took orders and was a popular preacher in his home county and later in London. In 1622 he was the incumbent at East Raynham where he benefited from a bequest by Anne Townshend. For a time he seems to have officiated at St. Mary's, Dover. In 1632 he came to London, and on 18 December 1633 was instituted to the vicarage of St. Stephen's, Coleman Street, vacated by the nonconformist secession of John Davenport. He himself sided with the puritans, and at that period inclined to independency under the influence of John Cotton.