[1] At the Battle of Pea Ridge on March 7 and 8, 1862, the battery was assigned to the command of Brigadier General Daniel M. Frost, along with Guibor's Missouri Battery and several units of the Missouri State Guard as part of the Confederate Army of the West.

After barely avoiding pursuing Union troops, the battery escaped with the rest of the Army of the West.

As part of Colonel Louis Hébert's brigade, the battery was engaged during early stages of the Siege of Corinth, and saw action at the Battle of Farmington on May 9.

[6] At the Second Battle of Corinth on October 3 and 4,[9] the battery was in the brigade of Colonel W. Bruce Colbert; Hébert had been elevated to division command to replace Little, who had been killed at Iuka.

[6] On October 5, the battery was engaged at the Battle of Davis Bridge, fending off a Union pursuit as the Confederates retreated from Corinth.

The 3rd Missouri Light Battery was positioned in the middle of the Confederate line and attracted heavy Union artillery fire.

When a Union infantry charge broke the Confederate line, the battery was unable to withdraw some of their pieces, losing either three[11] or one cannon to capture.

[6] At the Battle of Grand Gulf on April 29, 1863, the battery was stationed at a point 4 miles (6.4 km) away from Fort Wade on the Big Black River.

[13] After fighting at Champion Hill, the battery lost its cannons at the Battle of Big Black River Bridge on May 17; after which it entered the defenses of Vicksburg, Mississippi.

[14] At the Battle of Missionary Ridge on November 25, the battery was available, but did not see action; replacement cannons for those lost at Big Black River Bridge had not yet arrived.

For much of the rest of 1864, the battery guarded a portion of Mobile Bay, at one point firing at a Union Navy gunboat.