Disagreeing with his congregation on some points of church discipline, he gave up his post in 1672 and became a magistrate of the township. He died on 17 March 1696. John Woodbridge married Mercy Dudley, daughter of Governor Thomas Dudley and sister of Anne Bradstreet, on May 20, 1639, probably in Newbury, Massachusetts. They had twelve children. Dudley Woodbridge, judge-advocate of Barbados and director-general of the Royal Assiento Company, who died on 11 February 1721, and whose portrait was painted by Kneller, was probably their son. Woodbridge's younger brother Benjamin Woodbridge, who went to Massachusetts a few years after him, was the first graduate of Harvard College in 1642.