Since the colonial times, the church has been located in the Astilleros (Shipyards) area, which was created following the transfer from the Old City in 1690. It constitutes one of the first religious references of Guayaquil. Curiously, the pirates entered the little chapel several times to pray before looting the city. Later in time, La Industria Street, currently Eloy Alfaro Avenue, was opened, which was initially linked to the shipbuilding industry, reason why, some hardware stores that sell marine articles have remained in the place.
The Mercedarian Order built the building of wood, and its slim tower became a traditional image for this area located near the San Carlos Estuary, existing Olmedo Avenue, which have always been a commercial area.
A mist of legend and tradition remains in its cloister, which kept the vaulted ceiling and the Altarpiece of the Main Altar. The old walls and the entablature of the floor were replaced by concrete.
In 1786, priest Salvador Guerrero decided to build a temple to provide spiritual guidance to the people involved in the shipbuilding industry, which was growing rapidly. The initiative began to crystallize with the donation of the lot by a wealthy businessman of the city by the name of Severino Franco Espinoza. Alejo Franco gave the image of San Alejo as a gift.
At the entrance of Eloy Alfaro Avenue there is a legend that receives the visitor: “A young girl asked an image of Christ for a love miracle. In exchange she promised to donate the curls of her hair for the image to wear them. The miracle was granted and from then, the image of Jesus wears curls.
To the left, there is a group of statues crafted in the beginnings of the XX century, during the times of the confrontations between liberals and conservatives. Going forward there is a bell that belonged to one of the motorboats that covered the cocoa route from Guayaquil to Vinces.
The church keeps some admirable relics like: Santa Martha, the Virgin of La Merced, the Lord of la Porteria, the Lord of la Buena Esperanza and San Jose, which are the oldest and were crafted in the traditional Spanish style of the times of the colony. The figures have no body just a simple wooden structure from which the head, arms and feet emerge; fabric garments cover the structure. The are also jute and plaster figures, also from the colonial times, representing Santa Ana and San Joaquin; and made of wood like the Virgin of La Merced and the Lord of los Azotes, which were crafted by artisans from Guayaquil and Cuenca.