In Boston Saffin served for several years in the colonial assembly of the Massachusetts Bay Colony. He served as the speaker of that colony's assembly in 1684, the year in which the colonial charter was revoked. With the arrival of Joseph Dudley in 1686 and the establishment of the Dominion of New England, Saffin moved to Bristol (then part of the Plymouth Colony, now part of Rhode Island) in 1687. Following the Glorious Revolution in England in 1688, there was a revolt against the Dominion rule of Andros; Saffin sided with the rebels, and sat on the Plymouth Colony councils during the interregnum years from 1689 to 1692. This stance is likely responsible for a political estrangement between him and Dudley, who was among those imprisoned and sent to England.