During the conquest and settlement of the newly discovered Americas, an order of Franciscan missionaries attempted to convert the indigenous people, establishing a new church.

By 1770, the town had its own established church and included annexed areas such as Soyapango, Ilopango, and the San José Guayabal Valley.

In 1807, following a census done by Intendent Don Antonio Gutiérrez Ulloa, Tonacatepque was classified as a "pueblo" or small village, inhabited by 17 Spaniards, 718 natives, and 619 mestizos.

Almost seven decades later, on March 7, 1874, the Salvadoran Legislature (under the administration of Field Marshal Santiago González) authorized the reclassification of Tonacatepeque from "pueblo" to "Villa."

The new administrative district included the populations of Toncatepeque, Apopa, Ilopango, San Martín, Nejapa, Guazapa, Aguilares, and El Paisnal.