Like their father, all of Allen's sons were loyalists opposed the overthrow of British rule in the American Colonies.
Upon his resignation from the Continental Congress, he joined Howe's army as a non-combatant, and returned to Philadelphia during the British occupation.
He was a guest of Washington at Harlem Heights in November, 1776, and was summoned before the Committee of Public Safety for "disaffection."
William was one of the first officers commissioned by the Continental Congress, and served under Montgomery in the 1775 Canadian campaign.
Immediately after the adoption of the Declaration of Independence, however, he resigned his officer's commission in the Continental Army, and became the Lieutenant-Colonel of a regiment called the "Pennsylvania Loyalists," which he commanded throughout the war.