Goodwin was one of the earliest clerical supporters of the democratic puritans, and then of the army against the Parliament. His "Anti-Cavalierisme" (1642) proclaims the need of war to suppress the party 'now hammering England to make an Ireland of it.' The doctrine of the divine right of kings he assailed in his "Os Ossorianum, or a Bone for a Bishop", against Griffith Williams, bishop of Ossory. He also attacked the presbyterians as a persecuting party in his "Θεομαχία, or the grand imprudence of ... fighting against God" (1644). In May 1645 he was ejected from his living for refusing to administer indiscriminately in his parish the baptism and the Lord's Supper, setting up a covenanted community within his parish. Goodwin immediately set up an independent church in Coleman Street, which had a large following. William Taylor, his appointed successor at St. Stephen's, was in his turn ejected in 1649, to be restored in 1657. Goodwin obtained the use of the church, but with a diminished revenue. Among his hearers at this period was Thomas Firmin, who took down his sermons in shorthand.