Having been kept from the greater part of the French Revolutionary War by his book, Broughton resumed his active naval career on 23 June 1801, when he was given command of the 50-gun "Batavier" in The Channel. He served aboard her until the Peace of Amiens was ratified, in April 1802. In May, Broughton was given command of the 36-gun "Penelope", serving in the North Sea, an appointment that lasted until two days before his next command, the seventy-four, "Illustrious", on 30 May 1807. In her, Broughton continued service, seeing action at the Battle of the Basque Roads. After the battle, Lord Cochrane proclaimed that Admiral Gambier had not done enough to destroy the French fleet and Gambier demanded a court martial at which he was acquitted, despite Broughton speaking out against him.