At the close of the war, Howe served in the honor guard that stood watch over the corpse of Abraham Lincoln, and soon afterward was appointed as a member of the military commission that tried the Lincoln conspirators. Howe did not make any public comments on the conviction or hanging of Mary E. Surratt, but was not among the five officers who petitioned President Andrew Johnson to commute her sentence to life in prison. Both assignments may indicate that the Radical Republican faction in the Congress found him useful and sympathetic. He also served in the Freedmen's Bureau in 1865. Howe was mustered out of the volunteer service on July 15, 1866.