When "Suffren" was commissioned in Brest, she was assigned to the Escadre de la Méditerranée shortly afterwards. After arriving in Toulon, she became the flagship of its commander, Palma Gourdon, on 24 February. Two months later she carried the President of France, Émile Loubet, on a state visit to Naples. As time went by several defects were revealed in service, including the weakness of the underpowered capstan which was barely capable of raising the anchor in waters deep. Another problem was that the centre engine and its propeller shaft tended to overheat. Gourdon was relieved by Charles Touchard on 4 October 1905. During fleet exercises off the Îles des Hyères on 5 February 1906, "Suffren" accidentally rammed the submarine when the latter miscalculated the fleet's movements while manoeuvring into firing position. "Bonite" rose to periscope depth less than in front of "Suffren", but the latter managed to turn quickly enough while the submarine was crash-diving that "Suffren" only struck "Bonite" a glancing blow. This was enough, however, to breach two compartments abreast the ship's starboard engine room and she had to be docked for emergency repairs. "Bonite"s bow was crushed and several of her ballast tanks were ripped open. Only by rapidly dropping her weighted keel was the submarine able to avoid sinking. No casualties were suffered by either vessel. During the summer of 1906 "Suffren"s above-water torpedo tubes were removed. She then participated in an international fleet review in Marseille on 16 September.