Flatters was made a second lieutenant and posted to Algeria with the 3rd Zouaves. He was appointed lieutenant in 1855. In 1856 he was granted a request to transfer to the Arab Bureaus ("bureaux arabes"), which had been created by Marshal Thomas Robert Bugeaud to administer the indigenous population. Flatters did not serve in the Crimean War of 1853–56 or the Franco-Austrian War of 1859. In January 1863 he spent three month's leave in Paris. There he met and became engaged to the 19 year old Sara-Marie Le Gros, sister of a former schoolmate at Laval. Flatters was promoted to captain in 1864. He married Sarah Marie Legros (1845–1933) in Paris on 1 May 1864. Their son Étienne Paul Jean Flatters (1868–1950) would become a Brigadier General. Due to the rough conditions in Algeria his wife could not accompany him when he returned to Algeria, and for the next fifteen years they spent time together only when he was on leave or during the short periods when he was stationed in France.