Between October 1989 and May 1991, the boat undertook a major refit which revolved around upgrades to the level of the lead vessel in the class, Améthyste.

In September 2001, the boat torpedoed and sank a target ship, the decommissioned destroyer D'Estrées, off Toulon.

On 6 March 2015 it was reported that in a later erased blogspot of the French Ministry of Defence that during a training exercise off Florida Saphir, in her role as part of the "enemy" attack group, had "sunk" the aircraft carrier USS Theodore Roosevelt and its escort.

[6] In October 2020 it was announced that the submarine Perle would be repaired using the forward section of her decommissioned sister Saphir.

[7] The fanion of Saphir and the men's boat were decorated with the Cross for Military Valour with bronze palm on June 5, 2012.