In August 1862, learning of a violent Dakota uprising in the southwestern corner of the state (caused largely by the federal government's failure to deliver annuities in goods and payments on time, and resulting in the Dakota starving), Flandrau enlisted in the Union Army as a captain. He assembled an armed force and quickly went to the defense of settlers at New Ulm. Both Flandrau State Park and the community of Flandreau, South Dakota, are named in his honor, as he was successful in defending the community. Governor Alexander Ramsey appointed Flandrau in charge of the defense of the southwestern frontier of the state, and he served in this capacity at the rank of colonel for two years, simultaneous to his position on the Minnesota Supreme Court.