In 1870, Governor Henry C. Warmoth, elected as part of the Reconstruction-era civil government, appointed Flanders as Mayor of New Orleans. As of 2018, Flanders remains the most recent Republican mayor of the city. He was later elected to a full two-year mayoral term, serving until 1873. That year, President Ulysses S. Grant appointed Flanders as Assistant Treasurer of the United States. Flanders ran unsuccessfully in 1888 as a Republican candidate for Louisiana State Treasurer; by that time Democrats were controlling most statewide elected positions.