At the beginning of the Second World War "Protée" was assigned to the 3rd Submarine Division, based at Toulon, alongside her sisters , and . At the beginning of February 1940 the 3rd Submarine Division was briefly transferred to Casablanca to carry out surveillance of the Canary Islands, where a couple of German cargo ships were present. The submarine division was then assigned to the Mediterranean theatre on 12 April, first at Bizerte then, without the "Fresnel", at Beirut, under the authority the British commander-in-chief in Alexandria. "Protée"took part in several patrols in the Dodecanese until the signing of the armistice between France and Germany on 22 June 1940. On 25 June, the date the armistice came into force, the captain of "Protée" ignored an order to return to Beirut, and instead sailed to Alexandria, becoming part of Force X. The captain was chastised for this incident.