In late 1786, Allemand returned to France to benefit from a reform of the Navy by which he could obtain a permanent commission of sous-lieutenant de vaisseau for his service.

He was sent with two ships of the line and one frigate to raid British outposts in Labrador, and on his way back captured a convoy worth 80 million francs, making 1,800 prisoners including the Governor General of Canada, his family, and a number of officers, returning to Brest in November 1796.

After serving in office duties in 1802, Allemand received command of the Magnanime, in Admiral Missiessy's squadron, on which he departed on 11 January 1805 for the Saint-Domingue expedition.

On 22 June, Allemand was officially made chief of the squadron, and tasked with a diversion manoeuver that would bring him to rejoin Villeneuve's squadron in Ferrol: Allemand's expedition of 1805 was a vast commerce raid that led to the capture of 43 British merchantmen, the sloop-of-war HMS Ranger, the hired armed cutter Dove and the 56-gun HMS Calcutta.

[1] 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 river Charente after throwing part of her artillery overboard.

The resulting loss of four French ships of the line and one frigate 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.

In 1812, Allemand succeeded in bringing several warships from Lorient where they were trapped to Brest in order to form a larger French fleet.