Jordan was assigned to western frontier duty until 1846, when he was promoted to first lieutenant. In the Mexican–American War, he served creditably at the battles of Palo Alto and Resaca de la Palma. In 1847, he was promoted to captain and served as a quartermaster. He remained at Vera Cruz for a year after the war in an administrative role. He was next posted to various Southern garrisons and on the Pacific Coast.