While recovering from losing his arm, Fiser was assigned to recruiting duties. On February 26, 1864, he was promoted to the rank of colonel, but the wound was slow to heal and he resigned his commission on June 12 and returned home. That winter Maj. Gen. Lafayette McLaws asked for Fiser for service in South Carolina, and he rejoined the Confederate Army. In 1865 Fiser was given command of a brigade of reservists from Georgia, part of the scattered forces that opposed the Union soldiers of Maj. Gen. William T. Sherman during the Carolinas Campaign. On April 9 his small 800-man brigade was merged with that of Col. George P. Harrison, his senior, reducing Fiser to regimental command. Also in 1865 Fiser was appointed a brigadier general, however the Confederate Senate never confirmed his commission as such.