When Dudley was commissioned in 1686 to temporarily head the Dominion of New England, Stoughton was appointed to his council, and he was then elected by the council as the deputy president. During the administration of Sir Edmund Andros he served as a magistrate and on the council. As a magistrate he was particularly harsh on the town leaders of Ipswich, who had organized tax protests against the dominion government, based on the claim that dominion rule without representation violated the Rights of Englishmen. When Andros was arrested in April 1689 in a bloodless uprising inspired by the 1688 Glorious Revolution in England, Stoughton was one of the signatories to the declaration of the revolt's ringleaders. Despite this statement of support for the popular cause, he was sufficiently unpopular due to his association with Andros that he was denied elective offices. He appealed to the politically powerful Mather family, with whom he still had positive relations. In 1692, when Increase Mather and Sir William Phips arrived from England carrying the charter for the new Province of Massachusetts Bay and a royal commission for Phips as governor, they also brought one for Stoughton as lieutenant governor.