The weapon has been used by various teams as a side arm on 'normal' missions where the need for defence is greater than the need for capture, like all Tau'ri projectile weaponry. Curiously, while teams operating out of Stargate Command are seen sometimes armed with a Zat'nik'tel instead of the Beretta due to its versatility and nearly unlimited ammo; the teams in Atlantis, use the handgun more frequently.
The reason for this is unknown, considering the limited resources of the Atlantis base, the limit of ammunition, and the fact that the enemy that Atlantis reconnaissance teams are most likely to face, the Wraith, have healing abilities that take a considerable amount of damage before succumbing to their wounds. In one instance, it took Sheppard two magazines just to kill one Wraith, although he did so in a slow manner, giving the prisoner a limited amount of time to heal from his wounds before his death. Regardless, other than the weapons effectiveness in the Milky Way, the mystery of why the Atlantis expedition mostly uses the Beretta, despite its ineffectiveness, is unknown.