In 1979 it received the visit of the Catholic pontiff John Paul II, and was later declared —along with the entire Historic Center of Oaxaca— a World Heritage Site by UNESCO.

More or less at the same time, the site of the indigenous town of Huaxyacac was erected in Villa de Antequera, by decree of King Charles V, Holy Roman Emperor.

Later, in 1551, the town council granted the Dominicans some land located in the vicinity of the Cerro del Fortín hill for the purpose of building a convent.

Two earthquakes at the beginning of the 17th century (the first, in 1603, and the second, in 1604) destroyed the Convent of San Pablo of Oaxaca, a fact that motivated the acceleration of the works of Santo Domingo.

Four years later, the convent complex was formally inaugurated, and in 1623 the establishment was elevated to the category of university, where philosophy and theology courses were taught.

The Convent of Santo Domingo currently houses an important museum collection made up of historical objects from the state of Oaxaca.

It is located about half a kilometre north of the central squares of the city, the Zócalo and the Alameda, and the connecting street is pedestrianised, so it is a popular place for both tourists and local residents to stroll.