When Kearny departed with his forces for California, he left Colonel Sterling Price in command of U.S. forces in New Mexico. He appointed Charles Bent as New Mexico's first territorial governor. An issue more significant than the galling daily insults was that many New Mexican citizens feared that their land titles, issued by the Mexican government, would not be recognized by the United States. They worried that American sympathizers would prosper at their expense. Following Kearny's departure, dissenters in Santa Fe plotted a Christmas uprising. When the plans were discovered by the US authorities, the dissenters postponed the uprising. They attracted numerous Native American allies, including Puebloan peoples, who also wanted to push the Americans from the territory.

Provisional governor Charles Bent and several other Americans were killed by the rebels. In two short campaigns, United States troops and militia crushed the rebellion of the Hispano and Pueblo people. The New Mexicans, seeking better representation, regrouped and fought three more engagements, but after being defeated, they abandoned open warfare. Hatred of New Mexicans for the occupying American army combined with the oft-exercised rebelliousness of Taos residents against authority imposed on them from elsewhere were causes of the revolt. In the aftermath of the revolt the Americans executed at least 28 rebels. The Treaty of Guadalupe Hidalgo in 1850 guaranteed the property rights of New Mexico's Hispanic and American Indian residents.