In 1635 he was convened for breach of canons, but on his promise of amendment Bishop William Juxon took no further proceedings. In 1638 Goodwin broached from the pulpit of St. Stephen's his opinions on justification by faith, taking a view which was already regarded as practically Arminian; he always cited Calvin as bearing him out on some points. A pulpit controversy with other city ministers on this topic was calmed by Juxon, all parties agreeing to desist. Next year (1639) Goodwin angered his opponents anew by insisting on the need of a learned ministry. Juxon reported to William Laud that he did not despair of a good issue. Goodwin had a hand in drafting the London clerical petition against the new canons of 30 June 1640. Alderman Isaac Pennington was one of his parishioners, and joined his congregational society.