The temple is formed by a three nave Basilica–type floor layout, a central vault type cannon floor layout decorated with molding frames that include ornamentation with organic motifs. The colors where the naves are developed are rose, peach and Nile green.

The vault has four large hanging lamps plus some smaller ones in its supporting columns. The lateral naves are separated from the central one by columns that hold semicircular arches, decorated in their intrados with marble paint. Its capitals are crowned by an organic decoration similar to the one in the lamps. The semicircular dividing arches of the naves are large and open. The pulpit is in the center richly decorated with human and zoomorphic figures made in polychrome and gilded wood that holds the structure. Angelic beings act as caryatids, holding the whole set.

The lateral naves, differently from the central one are not vaulted but are rather in the post and dintel construction, decorated with moldings and ornaments with organic motifs. In the central nave division with the left lateral nave there is a reproduction of the Virgin de la Merced, located within a decorated coffin.

Through the ambulatory of the lateral naves we can find a series of wall niches containing altars dedicated to Biblical characters and saints that are the Church’s object of devotion decorated in an architectonic style, i.e. imitating small classic buildings decorated with columns, pillars, pilasters and topped by triangular or curved pediments, in original marble or rather with paint imitating marble, and with religious symbolism. Between each altar there is a small representation of the stations of the Holy Cross. Hence, there is in order: the left nave through the entrance to: Saint Pedro Armengol, Patron Saint of Children’s Orphanages; Saint Serapio; the mortal remains of Saint Pedro Armengol (altar completely made of marble); Saint Ramón Unborn, Patron Saint of future mothers; Saint Pedro Pascual and the altar dedicated to the Sacred Heart of Jesus, where the Side Chapel is located, safeguarded by two sculptures of kneeling angels.

In the front, on the lateral right nave, from the high altar there is the following: Saint Pedro Nolasco, founder of the community of the Mercedario Fathers; ensemble of Jesus, Mary and Joseph; set dedicated to Santa Teresa de los Andes, accompanied on both sides by Saint Judas Tadeo on one and Saint Cecilia on the other, each one separated by columns finished off by a frieze holding a curved pediment; sculptural set of the Crucifixion of Jesus; the Virgin of Lourdes; and finally Saint Expedito. The lateral right nave is also finished off with a pictorial work, this time dedicated to the Sacred Heart of Jesus.

The high altar has two large figures. The lower one is of Jesus resurrected who has a palm leaf in one of his hands. It is within a shrine held by four fluted Ionic style columns. The top figure is of the Virgin de la Merced, the second virgin arriving to Chile after the Virgin del Socorro, currently found in the Church of San Francisco, and after which this temple was named. She is surrounded by a construction held by columns and pilasters, smooth and fluted. The lateral sides are totally decorated with pastel tones in pale rose, apricot and Nile green and decorated with ornamental moldings.

One of the attractive points is the altar dedicated to the Virgin of Lourdes, since it is the only one of its type that rebuilds at a smaller scale the grotto where the appearance of the Virgin to Saint Bernadette occurred. The niche is completely covered with imitation rock in relief imitating the Lourdes Grotto, where the Virgin is in the center of this piece and on the lower left side is Saint Bernadette kneeling before the virgin.

The altars of Saint Pedro Pascual and the sculptural ensemble of Jesus, Mary and Joseph are also interesting. Both altars face each other in the lateral naves. They are not done in the traditional architectonic manner, but rather they have used the Trompe l’oeil technique, more commonly called “Trampantojo” in Spanish. This means that the bottom of the niche is painted with an architectonic imitation, simulating a perspective. This technique is first seen in the Roman Empire and its maximum splendor is during the XVIII Century, where the technique reached such heights that it confused reality with the fantasy of the painting.