After the Spanish conquest of Guatemala the town was in charge of the franciscans, who had convents and doctrines in the area covered by the modern departments of Sacatepéquez, Chimaltenango, Sololá, Quetzaltenango, Totonicapán, Suchitepéquez and Escuintla.

The "Provincia del Santísimo Nombre de Jesús" (English:"Province of the most Holy Name of Jesus"), as the Franciscan area was then called, reached up to 24 convents by 1700.

[10] When the State of Guatemala was created on 11 October 1825, after independence from Spain, San Pedro Yepocapa was established as town, and then was raised to a municipality of the Chimaltenango District by a decree from 12 September 1839.

On 15 October 1974, tremors woke up people in the settlements surrounding the Volcán de Fuego at 2:00 AM, followed by rumbling and cinders and ashes falling from the sky, which submerged the town into darkness for a few days.

[5] San Pedro Yepocapa was one of the most impacted towns, ending under more than 1m of ash after the four days that the eruption lasted; approximately 1100 people from Morelia hacienda and annexes had to be evacuated to temporary shelters in neighboring Santa Lucía Cotzumalguapa, Escuintla or Patulul, Suchitepéquez.