After declining a regular Army commission, Belknap was appointed Iowa's Collector of Internal Revenue by President Andrew Johnson; he served with distinction for four years. In 1869, President Ulysses S. Grant appointed Belknap as Secretary of War. During his tenure, Belknap ordered portraits of all the previous Secretaries, intending to create a complete collection in honor of the United States Centennial. In 1871, Belknap was investigated by Congress, after he was directly involved in the sale of arms and munitions to France, while the United States was ostensibly neutral during the Franco-Prussian War. The same year, Belknap had arranged aid for victims of the catastrophic Chicago Fire. During the Reconstruction Era, Belknap's War Department and the U.S. military worked under the supervision of President Ulysses S. Grant and the United States Attorney General's office to occupy the former Confederacy and attempt to implement changes in government and the economy, while protecting freedmen from an increasingly violent insurgency. Belknap supported Grant's Reconstruction policy, which most Democrats opposed.