Oñate was born in 1550, at Zacatecas in New Spain (colonial México) to a family of Spanish-Basque colonists and silver mine owners. His father was the conquistador and silver baron Cristóbal de Oñate, a descendant of the noble house of Haro. His mother was Doña Catalina Salazar y de la Cadena.[7] His ancestor Cadena fought in the 1212 Battle of Las Navas de Tolosa in Al-Andalus, and was the first to break through the line of defense protecting Mohammad Ben Yacub. The family was granted another coat of arms, and thereafter were known as “Cadenas”.[8]
Juan de Oñate married Isabel de Tolosa Cortés de Moctezuma, granddaughter of Hernán Cortés, the conqueror of the Triple Alliance, and the great-granddaughter of the Aztec Emperor Moctezuma Xocoyotzin.[9