La Merced was deemed a national monument in 1956, as its walls house memories of the dead city. Those walls were witness to the future conquerors of Peru on December 28, 1530, and the historic sermon from the lips of the priest Juan de Vargas on the conquest of Atahualpa's grand empire.
The church preserves its original stone façade in the baroque style. It is located on Central Avenue very close to what was the Earth Door that gave main access to the city; the front area and courtyard of La Merced was literally the reception area of the walled enclosure. In accordance with the common design in Old Panama, it has three soaring naves, a roof supported by towering wooden pillars, and a Moorish molding dating to the colonial era. There are two towers, both topped with cupolas.
The front plaza is flanked by two small chapels, one designed for veneration of the Virgin of La Merced. A European portrait of the Virgin of La Merced that hangs in the chapel is one of the oldest paintings in the country and dates to the year 1600. After Old Panama was plundered in 1671, the portrait was rescued by a devotee and transferred from the convent. The other chapel is the current mausoleum for the Pérez Arosemena family.
The temple interior was remodeled and the main altarpiece had to be renovated after a fire in 1963. An important image of Our Lady of Mercy was donated by Charles V and brought from Spain in 1722. The original columns, made of loquat wood, are currently under renovation. This church is the guardian of a relic of St. Pancras, storing part of the saint's ankle bone, as well as an image of Our Lady of Charity, patron saint of Cuba.
The church's sacristy houses a museum with collections of imagery, colonial paintings, gold and silver objects, and the following important Panamanian historical religious documents: the Act of Consecration of the Metropolitan Cathedral of the New Panama from 1796 and registries of births, baptisms, marriages, and deaths of notable people of the era, the most prominent being the baptismal record of General Tomás Herrera, the marriage and death certificates of the First President of the Republic Manuel Amador Guerrero, and the marriage certificate of the poet Ricardo Miró. In addition, there are objects belonging to the clergy, most notably the silver crosier that belonged to the religious devotee to Our Lady of Mercy, friar José Higinio Durán y Martel, who signed the declaration of independence from Spain in 1821 as a representative of the church.
A replica of the 1904 Constitution of the Republic of Panama is stored in the museum at La Merced, in addition to an interesting chronicle written by the Panamanian businessman Camilo Quelquejeu Araúz about the events of the Battle of Calidonia Bridge that lasted from July 19 - 26, 1900.