In 1809, Allemand was vice-admiral and commanded the squadrons of Brest and Rochefort. His insufficient defensive dispositions allowed the British to launch a fireship attack on his squadron at anchor, starting the Battle of the Basque Roads. Allemand reacted to the attack merely by giving his captains their liberty of manoeuver and concentrating on the safety of his own ship, the 120-gun "Océan", which sailed to the haven of the Charente River after throwing part of her artillery overboard. The resulting loss of four ships and two frigates was blamed on captains, four of whom were court-martialed with one relieved of duty and one executed by firing squad, but Allemand's role was never questioned, much to the outrage of the officers. Allemand was quickly transferred to the command of the Mediterranean fleet to prevent possibility of his hearing by the court of Rochefort.