When The United States acquired northern New Mexico in 1848, it inherited the entire burden of protecting traffic on the Santa Fe Trail and in the Southwest. By 1851 almost 1,300 soldiers were stationed at eleven outposts in New Mexico Territory, but the Secretary of War was not satisfied with their performance and ordered the posts consolidated near the junction of the two branches of the Santa Fe Trail. The move improved the Army’s effectiveness against Indian raiders, but the fort’s log construction was unsuited to the northern New Mexico climate. It was torn down in 1867 and replaced by adobe buildings housing the Fort Union Arsenal.
Shortly after the Civil War began, construction started on the second fort, a star-shaped fieldwork based on a French design and considered virtually impregnable. The impregnability of the second fort was never tested. In 1862, Brigadier General Henry H. Sibley led Texas volunteers into New Mexico to take Union military posts and advance Confederate efforts to annex territory from Texas to California. After victories at Valverde Ford, Albuquerque and Santa Fe, Sibley moved on Fort Union, but his supply wagons were intercepted and destroyed at Glorieta Pass by a detachment of Colorado Volunteers commanded by Major John Chivington, who led the Sand Creek Massacre two years later.
The third Fort Union was begun in 1863 and completed in 1869. It was the largest and most expensive of the Indian Wars-era forts, including the arsenal the military post, and the quartermaster depot that supplied the entire Military Department of New Mexico.