In 1660, during the Restoration, he escaped with his father-in-law, General Edward Whalley, to Massachusetts. They landed in Boston on 27 July 1660, and settled in Cambridge. When the news arrived in Boston, on the last day of November, that the act of indemnity passed by parliament in August excepted them from its provisions, the government of the colony began to be uneasy, and a meeting of the council was held on 22 February 1661 to consult as to their security.

Four days later, the two fled for New Haven, Connecticut, arriving on 7 March 1661. There John Dixwell, also condemned as a regicide, was living under an assumed name. They were housed by Rev. John Davenport. After a reward was offered for their arrest, they pretended to flee to New York City, but instead returned by a roundabout way to New Haven. In May, the Royal order for their arrest reached Boston, and was sent by the Governor to William Leete, Governor of the New Haven Colony, residing at Guilford. Leete delayed the King's messengers, allowing Goffe and Whalley to disappear. They spent much of the summer in Judges' Cave at West Rock.

Letters to Dr. Increase Mather and others give hints as to Goffe's whereabouts, but very little is clear, perhaps due to his desire not to be captured and executed. He appears to have passed the rest of his life in exile in New England, separated from his wife and children, under one or more assumed names.

Tradition has him sheltering for a decade in the home of Rev. John Russell at Hadley, Massachusetts, reappearing, according to legend, to lead the town's defence during King Philip's War, giving rise to the legend of the Angel of Hadley. After the war in July, 1676, Goffe is last seen in Hadley and went off into Hartford and was nearly arrested in 1678 by being recognized but once again escaped in time. By 1679, no record of Goffe’s whereabouts are and was presumed dead shortly after.

Another traditional account has him later living in Stow, Massachusetts under the alias of John Green, where his sister Mary [Green] Stevens resided, dying in Stow, and being buried in the Stow Lower Cemetery under an unmarked granite slab. However, his dying in Stow is debunked: in fact, Mary [Green] Stevens was the sister of Capt John Green who died in Stow in 1688. Another legend is that he died in Hartford, Connecticut under an alias about 1680. A Phillip Goffe settled in Wethersfield, Connecticut prior to 1649, where his granddaughter Mabel Goffe in 1707 married Daniel Andrews; allegedly Mabel Goffe was a descendant of William Goffe. However, this is unlikely as of William Goffe's children only two married and had issue: a daughter Frances; while Williams Goffe's surviving son Richard and his descendants were residents of Waterford, Ireland. Burke's Peerage reports that William Goffe died in New Haven, Ct in 1680.

The three regicides are commemorated by three intersecting streets in New Haven ("Dixwell Avenue", "Whalley Avenue", and "Goffe Street"), Hadley, and in some neighbouring Connecticut towns as well.