The military models were equipped with a 7.62 mm (.30 in) ShKAS machine gun, and later with a 12.7 mm (.50 in) UBK heavy machine gun.
IS-2 – The second airframe with improvements and M-88 engine in a long-chord NACA cowling, armed with 2x BS and 2x ShKAS.
3 × 7.62 mm (0.30 in) rear-firing ShKAS machine guns (later replaced by 12.7 mm (0.50 in) Berezin UB machine guns) in the canopy, dorsal and ventral hatches.
A single synchronised UBS 12.7 mm machine gun and wing racks for two 100 kg (220 lb) bombs comprised the aircraft's armament.
The first 197 Yak-3 were armed with a single 20 mm ShVAK cannon and one 12.7 mm UBS machine gun, with subsequent aircraft receiving a second UBS for a rate of fire of 2.72 kg (6.0 lb) per second using high-explosive ammunition.