Discalced Carmelites arrived in Chile in December 1689 from the Carmel monastery of San José de Chuquisaca, Upper Peru (today Sucre, Bolivia), at the request of the inhabitants of Santiago to atone for the desecrations and sacrileges committed in La Serena by the English pirate, Bartholomew Sharp in 1680, who sacked the churches and set fire to the city.

The King of Spain, Charles II, granted the licenses and established the first Carmel in Santiago on January 6, 1690, the Carmel Monastery of San José.

Later, in 1762, the Chief Magistrate of Santiago Luis Manuel Zañartu asked King Charles III of Spain to found a convent of the Carmelite nuns in La Cañadilla district, on the north bank of the Mapocho (today Av. Independencia). In July 1766, the King granted Royal License to build said monastery whose works began in October 1767 and finished in October 1770. The work was fully funded by the founder.

The patronage of the monastery was by Saint Raphael the Archangel and the church dedicated to the Blessed Mother of Carmel. Thus, the Carmel Monastery of Saint Raphael is founded.

Four Carmelites came out from the Monastery of Saint Joseph, and they were later joined by six Santiaguinas. A few years later the convent already had 21 sisters.

In 1783, the convent faced a great flood and overflow of the Mapocho River which caused great damages in the adobe walls of the monastery. The story tells that the image of the Virgin of Sorrows miraculously floated on the waters, with two candles lit on the sides. Currently, this image is in the Carmelite community in La Reina. As a result of this flood, the Carmelites had to leave the monastery momentarily and were received by the fathers of the Recoleta Dominica, which is why the nuns are so grateful to that congregation.

Another great flood in 1827 and the strong earthquake of 1850 increased the damages already present in the walls and also had serious effects on the foundations and the tower of the church.

In 1870, architect Fermín Vivaceta made some changes in the church, refurbishing the façade and structure, as well as building a new tower crowned by Saint Raphael the Archangel.

In 1887, this community gave rise to the foundation of the first Grotto of our Lady of Lourdes. The first image was taken from this church to the grotto and on the way the Holy Virgin, working miraculously, returned the sight to a blind man.

As the city grew, these neighborhoods became very noisy, causing the Carmel of San Rafael to move to La Reina in 1958, where the nuns live their silent lives in prayer.

The church and monastery were declared a National Monument in 1983 and, since 1985, they house the headquarters of the Episcopal Vicariate (North Area) of the Archbishop of Santiago.

The church is currently damaged as a result of the 27F earthquake and is closed to the general public.