The BMD-3 is equipped with a two-man turret which is armed with a 30mm 2A42 dual-feed automatic cannon and one 7.62mm PKT coaxial machine gun. The turret is fitted with weapons stabilizer 2E36-3 and manual weapons laying drives. Turret traverse is through a full 360º with weapon elevation from -5 to +75º. The high elevation allows it to be used against low- and slow-flying aircraft and helicopters. The effective range when firing AP-T (Armour-Piercing - Tracer) ammunition is 2,000 m, and when firing HE-I (High-Explosive - Incendiary) rounds the maximum range is 4,000 m. An Anti-Tank Guided Weapons Launcher (ATGW) 9P135M AT-4 or AT-5 is mounted on the top center of the turret. The latest versions of the AT-4 `Spigot' have a maximum range of 2,500 m while the AT-5 `Spandrel' has a maximum range of 4,000 m. The AT-4 launcher can fire 9M113 and 9M111 missiles. The anti-tank weapons guidance and control system is semi-automatic, two-channel. The ATGW system enables the crew to engage targets from the vehicle or with the system deployed at some distance away from it. Mounted at the front of the BMD-3 on the left side is a 30 mm AGS-17 automatic grenade launcher while in the right bow is a 5.45 mm RPKS machine gun. Each of the bow weapons is operated by one of the infantry seated in the front of the BMD-3 and covers the frontal arc. The 5.45 mm RPKS MG has a high rate of fire for use in the direct role whereas the 30 mm AGS-17 automatic grenade has a higher trajectory and can be used to suppress targets at ranges out to 1,200 m using HE fragmentation grenades. If required, these weapons can also be quickly dismounted for use in the ground role. Mounted on either side of the turret is a bank of three 81 mm electrically operated smoke grenade dischargers firing forwards. The BMD-3 can create its own smoke screen by injecting diesel fuel into the exhaust.

The hull and the turret of BMD-3 are made of all-welded aluminum which provides protection against the firing of small arms and shell splinters. In the middle of the hull, there are three seats for mounted infantrymen, one stowage rack for three 9M111 anti-tank missiles, three racks for ammunition boxes, and a filter-ventilation unit. The commander is seated on the right of the turret and has a cupola with a forward-opening hatch cover, while the gunner is seated on the left and has a single-piece hatch cover that opens to the front. Two of the five infantry are seated at the front, one on either side of the driver, with the other three seated in the fighting compartment near the turret, one firing port provided on each side of the hull. Another three infantry can be seated for short distances to the immediate rear of the turret with the roof hatch open.