Work began on a new cathedral designed by master architect Martín Casillas, which was commissioned in 1561 by King Felipe II, but progressed slowly because of scarce funds.

Finally in April of that year, the Blessed Sacrament was moved from the former church to the new one; however, it would not be consecrated until October 12, 1716.

After years of remaining damaged, Bishop Diego Aranda contacted to Manuel Gómez Ibarra for the design of the new towers.

Current threats include a slight tilt of the north tower and structural damage to the dome.

The cathedral houses the mummified body of Santa Innocencia (a young girl from the 1700s who, according to legend, was killed by her father for converting to Catholicism),[5] well as the remains of three cardinals and several other former bishops of the diocese, and Fr.

The cathedral is built using adobe, yellow stone quarry and tezontle, a volcanic rock typically red in color, that is commonly used in Mexico .

The dome at the rear end of the cathedral is decorated with stain glass depicting various biblical scenes.