Oñate was born in Zacatecas, Mexico, the son of a wealthy mining magnate. He studied at the University of Mexico and served as a military captain in the Spanish army. In 1595, he was appointed governor of New Mexico by the viceroy of Mexico, Luis de Velasco.
Oñate led an expedition of over 400 people, including soldiers, settlers, and missionaries, into New Mexico in 1598. He founded the first Spanish settlement in the region, San Juan Pueblo, and established a capital at San Gabriel. Oñate also explored the Rio Grande Valley and the surrounding area, and made contact with several Native American tribes.
Oñate's rule in New Mexico was marked by both conflict and success. He had a reputation for cruelty and violence, and was accused of mistreating the Native Americans. However, he also founded several permanent settlements and established a lasting Spanish presence in the region.
In 1614, Oñate was recalled to Mexico by the viceroy after receiving numerous complaints about his behavior from Native Americans and settlers. He returned to Spain in 1620 and died in poverty in Madrid in 1626.