[5] The cathedral has more than 400 years of history, however there are not enough historical documents such as plans or drawings that speak about the construction process of the building through time.

In the same way, various investigations and thanks to the Historical Archeology inside the building, it has been possible to better understand its history and the various changes and reconstructions that it has had over the centuries By the seventeenth century the city lacked a large temple, since the only cathedral in the city was the Iglesia de la Merced, so in 1563 permission was requested to build a larger temple that would function as another cathedral of the town of Comayagua.

According to data from the Honduran Institute of Anthropology and History (IHAH), around 18 indigenous peoples worked on the construction of the Catholic monument.

Over the centuries, graves were made inside the temple, according to the local researcher and historian Tirso Zapata, among the deceased who are inside the cathedral are that of the bishops Don Juan Merlo de la Fuente and Fray Gaspar de Andrade which in the sixties, their bodies which possessed a cadaverous incorruptibility, were exposed to the general public in glass urns, but in 1963 the late Monsignor Bernandino Mozzarella ordered to hide them so they never became exhibited.

At the beginning of this century, it was fully restored as part of the rehabilitation project of the historic center of the city, a work directed by the IHAH, with the collaboration of the Spanish Cooperation Agency.

On the main altar you can see a gilded wooden altarpiece, with a carving of the image of the Immaculate Conception and an crucifix made in 1620 by the Spanish artist Francisco de Ocampo and donated to the city by King Felipe II of Spain.

In the tower of the cathedral there is also the oldest clock in the Americas, built by the Arabs during their occupation in Spain in the Middle Ages around the year 1100.

Before it was transferred to the Americas, it was working in the Alhambra, the Arab palace in the city of Granada, the capital of the last Muslim kingdom of the Iberian peninsula.

The clock mechanism is based on gears, ropes, weights and a pendulum, the whole set shows the time on the dial located on the facade of the church where the number 4 in Roman numerals is shown as IIII and not as IV.

During 2007 it was subjected to a restoration process by the Municipal Mayor's Office, the National Congress, the Comayagüense Cultural Committee and the supervision of the Honduran Institute of Anthropology and History, for which the master watchmaker Rodolfo Antonio Cerón Martínez from Guatemala was located, who after five months of hard work concluded his work on December 20, 2007.