Allen participated in all the battles in which his regiment took part except a few minor ones, due to wounds he received in battle. During the Battle of Cold Harbor, the bones in his wrist were shattered, and he later incurred a flesh wound in the same wrist at the First Battle of Fort Fisher. He was also wounded in the leg near his ankle at Fort Fisher; the musket ball remained there until his death. While recovering from injuries, he was reassigned to New York to recruit new soldiers. He was promoted to the rank of major in June 1864, and, for "meritorious conduct" at Fort Fisher, he was recommended for promotion by President Lincoln and brevetted lieutenant colonel on March 13, 1865.