In 1775 Nixon had moved to Sudbury, Massachusetts, and was a captain of the town's Minutemen whom he led at the Battles of Lexington and Concord.
In August 1776, Nixon was promoted to brigadier general, and he commanded a brigade consisting of the 3rd, 5th, 6th and 7th, and 8th Massachusetts Regiments.
He led his brigade in the Battle of Harlem Heights and later in the Saratoga Campaign, when it was reinforced by Cogswell's, Gage's and Mays's regiments of Militia.
Nixon's brigade was involved in the Battle of Bemis Heights in October 1777, and took part in the final assault; during this attack a cannonball passed so close to his head that his sight and hearing were affected the rest of his life.
Nixon moved to Weybridge, Vermont in 1806 and died while visiting his son in Middlebury on March 24, 1815.