At the beginning of the Second World War Protée was assigned to the 3rd Submarine Division, based at Toulon, alongside her sisters Achéron, Fresnel and Actéon.

[1] 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.

The French Navy long thought that the loss of Protée was due to a surface engagement with a German naval vessel.

[7] However a dive conducted in 1995 confirmed the theory developed by the United States Navy in the 1950s that the submarine's loss was caused by striking a mine.