With the outbreak of the Civil War, he was commissioned as a brigadier general in the Federal Missouri State Militia on November 27, 1861.

General Loan participated in counter-guerrilla operations, including the victory against Colonel John A. Poindexter's irregular cavalry at the Battle of Yellow Creek on August 13, 1862.

[1] He was appointed by President Ulysses S. Grant as a member of the board of visitors to the United States Military Academy in 1869.

He resumed the practice of law in St. Joseph, Missouri, and served as delegate to the Republican National Convention in 1876.

Benjamin Loan died in St. Joseph, Missouri, and was interred in Mount Mora Cemetery.