In May 1864 he was transferred to command the Artillery during the siege of Petersburg. On December 12, 1864, President Abraham Lincoln nominated Abbot for appointment to the grade of brevet brigadier general of volunteers to rank from August 1, 1864 and the U.S. Senate confirmed the appointment on February 20, 1865. In December 1864 he was placed in command of all siege artillery in the Army of the Potomac and Army of the James that were besieging Petersburg. In January 1865 General Alfred H. Terry requested General Abbot accompany his expeditionary force to Fort Fisher. Abbot commanded a provisional brigade of siege artillery during the successful Second Battle of Fort Fisher.