At West Point, Mouton was an average student scoring good marks in certain areas, including French, but it was evident that he struggled with the new language he was around. Alfred graduated from West Point on July 1, 1850, 38th out of 44. He stayed with the United States Army just briefly before resigning his commission that September. As soon as he resigned his commission, Mouton took up a civil engineering position as an assistant engineer for the New Orleans, Opelousas and Great Western Railroad. He held that position from 1852 to 1853. After resigning from the railroad business, Mouton took up farming sugar cane in Lafayette Parish, Louisiana.