The whole eastern half of New Mexico was claimed by the breakaway Republic of Texas in 1836, but was not occupied by American troops until the arrival of Stephen W. Kearny and his Army of the West in 1846.

The settlement, of Hispanos from elsewhere in New Mexico and local Puebloans, was well established by 1843, when there was a raid on the town by freebooters from the Republic of Texas under Colonel Charles A. Warfield,[5] claiming that the people in Mora had purchased stolen Texan cattle from the Comanche.

The town, then consisting of the two settlements of Upper and Lower Mora,[9] (sometimes misspelled "Moro" in American documents of the era) was the site of two armed conflicts between United States Army troops and a militia of Hispano and Puebloan Mexican-nationalists, in the Taos Revolt, a guerrilla campaign of the war.

In the First Battle of Mora, on January 24, 1847, a group of over 150 New Mexican resistance fighters repelled an expedition of 80 US Army troops and killed their commander, Captain Israel R. Hendley, and several others.

This destruction has made historical and genealogical research on Mora difficult earlier than 1848, because most early records went up in flames with the buildings.

The US Army controversially built Fort Union in 1851 on private Mora Grant land in the valley, along the Santa Fe Trail; while this sparked decades of unresolved legal actions, local farmers sold crops to the fort, which was a new and reliable source of income to the community, and the population swelled.

Ceran St. Vrain, an American veteran of the Taos Revolt (originally from St. Louis in what was then the French Upper Louisiana Territory), settled in Mora in 1853; he built a grist mill, and became a major supplier of flour, grain, and fodder to the fort.

The settlement is mentioned in Willa Cather's 1927 historical novel Death Comes for the Archbishop (Book Two, Chapter 2), about the establishment of the Roman Catholic Archdiocese of Santa Fe.

[citation needed] Frank Waters' 1941 novel People of the Valley takes place high in the Sangre de Cristo Mountains where an isolated Spanish-speaking community (based on Mora) confront a threatening world of change.