Anderson was then appointed assistant adjutant general to Maj. Gen. W. H. T. Walker of the Georgia State militia located in Pensacola, Florida.

In early 1863 he and was placed in command of nearby Fort McAllister,[4] located just downriver from Savannah, Georgia to help slow the advancing Union ironclads.

General P. G. T. Beauregard in his official report to the war department, commended very highly the conduct of officers and men engaged in the successful defense of Fort McAllister in February 1863.

General Anderson was appointed by President Rutherford B. Hayes to the Board of Visitors, US Military Academy at West Point in 1879.

As a member of the board, he chaired the committee for academics and discipline, and working alongside General "Fighting Joe" Wheeler helped reunite old friends, and assisted with reconciliation efforts.

As Police Chief, Anderson employed mostly veterans from both sides of the civil war in his force, putting his words of reconciliation into action.

An estimated seven thousand people attended the unveiling of a copper and granite monument, crowned with a bust of the general at Bonaventure Cemetery in February 1894.

[8] His son Robert Houstoun Anderson Jr. also served in the U.S. Army with distinction on the Mexican border, and in China before his death due to disease in the Philippines in 1901.