On November 28, 1862, Beattie was mustered at the age of 29 into the New York 26th Independent Battery (Light Artillery) as a 2nd Lieutenant. He was promoted to Vice First Lieutenant, then Captain of the Battery, by George W. Fox on March 29, 1863. He was honorably discharged on September 12, 1865 and mustered out at New Orleans. He returned to his family in Seneca, New York. He and his first wife, Mary E. Johnson, had a son, Willard Grant Beattie, in 1865.