Henry Nowell served as Deputy Governor of the Isle of Man under his brother Colonel Roger Nowell, the Governor appointed by the 8th Earl of Derby. He presided over the trial and execution of William Christian (Illiam Dhone) in 1662-1663. His private correspondence, preserved in the Kenyon Papers at Lancashire Archives, shows he considered the outcome predetermined before proceedings began. After the execution, he evaded the Privy Council's summons by hiding in Lancashire and eventually returned to the Island, where he spent the rest of his life.