Both Joseph and John Warren were active Freemasons. John served as Grand Master of the Massachusetts Grand Lodge (Antients) for two non-consecutive terms, 1783–84 and 1787-88. He was reelected in 1788, but declined the honor. John was present in 1792 when the Massachusetts Grand Lodge and St. John's Grand Lodge (Moderns) united to form the Grand Lodge of Masons in Massachusetts, and installed John Cutler as the first Grand Master of the united Grand Lodge. John Warren Lodge in Hopkinton is named after him.