Desaix took part in the First Battle of Algeciras in Algeciras Bay on the coast of Spain on 6 July 1801 as part of a French squadron under the command of Charles-Alexandre Léon Durand Linois, who formed his squadron into line of battle with his ships 500 yards (460 meters) apart and his flagship, the 80-gun ship of the line Formidable, at the northern end, with Desaix behind her.

Meanwhile, the British 74-gun third rate ship of the line HMS Venerable under Captain Samuel Hood, opened fire on Desaix at long range at 08:50.

[3] At 09:15, Saumarez's flagship, the 74-gun third rate ship of the line HMS Caesar, anchored in the bay and joined the action, also firing on Desaix.

[4] When a light breeze began to blow in from the northwest, Linois ordered his ships to sever their anchor cables and maneuver into better defensive positions close inshore, but Desaix ran aground directly in front of Algeciras during the maneuver.

Desaix was refloated, repaired, and returned to service after the battle, but in January 1802 she was wrecked at Saint-Domingue while trying to enter Cap Français harbour.