Trapier was promoted to the rank of brigadier general on October 21, 1861. He was given command the District of Middle and Eastern Florida from November 5 until March 14 of the following year. He then was ordered to the Western Theater and Gen. Albert Sidney Johnston's Army of the Mississippi, with Brig. Gen. Joseph Finegan taking over his district command in April. Trapier was assigned to lead the 4th Brigade of the 2nd Division in Maj. Gen. Braxton Bragg's II Corps in March. Gen. Beauregard assumed command of the Army of the Mississippi upon Johnston's death at Shiloh and led it during the First Battle of Corinth in late April.