By 1862 the 4th Kansas Infantry had never been completed and the existing soldiers were merged with those of the 3rd Kansas Infantry and 5th Kansas Infantry to form the 10th Kansas Infantry. The 10th Kansas was mustered into service on April 3, 1862 with William F. Cloud (from the 2nd Kansas Cavalry) as colonel; Weer was ordered to take command of the regiment on June 1, 1862. His regiment was attached to the Department of Kansas and as ranking officer he assumed command of that department's 2nd Brigade. He led his brigade at the First Battle of Newtonia under the overall command of (now brigadier general) Frederick Salomon. In October 1862 Weer assumed command of the 2nd Brigade in Blunt's 1st Division of the Army of the Frontier. He commanded this brigade at the battles of Old Fort Wayne, Cane Hill and Prairie Grove. In Blunt's official report on the action at Prairie Grove he praised Weer for behaving with 'gallantry, leading men into the thickest of the fight'. Shortly after the battle, Blunt left Weer in command of the 1st Division, which he commanded for a short while into 1863.