After Shiloh, General Jacob G. Lauman was transferred to command the brigade and Pugh returned to command of his regiment. He led his unit in the subsequent Siege of Corinth and the Battle of Hatchie's Bridge. When General Lauman was elevated to command of the 4th Division, Pugh again assumed command of the 1st Brigade. Pugh's brigade and the rest of the division were assigned to the XVI Corps during the Siege of Vicksburg and the following expedition against Jackson, Mississippi. During the Jackson Expedition, General Lauman ordered Pugh to make an attack against Brig. Gen. Daniel W. Adams' entrenched brigade. This attack resulted in heavy casualties for Pugh's brigade and Lauman was subsequently relieved of command.