A main descent engine was used to slow the craft until it reached a cutoff point, which was determined by the on-board computer based on altitude and velocity.

After two orbital adjustments were performed on 18 and 19 September the perilune was decreased to 15.1 km, as well as the inclination altered in preparation for landing.

At perilune at 05:12 UTC on 20 September, the main braking engine was fired, initiating the descent to the lunar surface.

Less than an hour after landing, at 06:03 UT, an automatic drill penetrated the lunar surface to collect a soil sample.

Three days later, on 24 September, after a direct ascent traverse with no mid-course corrections, the capsule, with its 101 grams of lunar soil, reentered Earth's atmosphere at a velocity of 11 kilometers per second.

Analysis of the dark basalt material indicated a close resemblance to soil recovered by the American Apollo 12 mission.

Luna 16 was a landmark success for the Soviets in their deep-space exploration program; the mission accomplished the first fully automatic recovery of soil samples from the surface of an extraterrestrial body.