Beauregard was transferred to the Western Theater to serve as second-in-command to General Albert Sidney Johnston. This move placed him in a strategically important area.

After General Johnston's death on the first day of the Battle of Shiloh, Beauregard assumed command of the Confederate forces. Although the Confederates initially achieved success, they were ultimately forced to retreat. The battle was a tactical draw but a strategic victory for the Union.

Due to overwhelming Union forces and logistical challenges, Beauregard evacuated Corinth, Mississippi, a vital Confederate supply hub. This decision drew criticism and led to his temporary suspension from command.