In March, 1864 Pederson joined the Scandinavian Regiment in Wisconsin. In May, 1864 was involved in the battles of Rock Face Ridge, Resaca before being captured at Pickett's Mill. He was taken to Andersonville Prison, Georgia, where he suffered from dysentery and scurvy.
Pederson was helped to escape by a Danish soldier in the Confederate Army. However, they were recaptured and Pederson was punished by being hung by his thumbs, whereas his friend from Denmark was executed.
After the war Pederson married Dorothea Larson and farmed in Bonduel, Wisconsin. The father of five children, Soren Pederson died on 19th January, 1911, while visiting his eldest son in Ellenbro, California.