 In October, 1863, he was made Lieutenant Colonel of the 7th United States Colored Infantry and later promoted to the command of the 41st United States Colored Infantry, both colored regiments under the Bureau of Colored Troops.With the 41st USCT, Haskell engaged in the Siege of Petersburg and Appomattox Campaign and was present at the surrender of Confederate General Robert E. Lee and the Army of Northern Virginia at Appomattox Court House on April 9, 1865.By the end of the war, he had risen to the rank of Brevet Brigadier General of volunteers.