Twombly carried his regiment's colors during the April 1862 Battle of Shiloh and participated in the Siege of Corinth, Mississippi as an acting second lieutenant. In October 1862, Twombly received a knee injury during the Second Battle of Corinth. He was hospitalized and placed on leave for six weeks to help him recover from the injury. In 1863, Twombly's regiment was formally stationed in Corinth, and engaged in numerous actions against the cavalry forces of Confederate General Nathan Bedford Forrest.