He inherited his father's baronetcy and lands in 1774. Sir John moved to Canada during the American Revolutionary War with family and allies, as he was at risk of arrest by rebel authorities. He led the King's Royal Regiment of New York and was promoted to brigadier general in 1782. That year Sir John Johnson was also appointed as Superintendent General and Inspector General of Indian affairs of First Nations in Canada, including the four Iroquois nations that had relocated there. After the war, he was appointed by the Crown to distribute lands in Upper Canada to exiled Loyalists, and estimated he helped resettle nearly 3800 in 1784. He also served in the Legislative Council of Lower Canada.