The current temple has always had an instrument to accompany the religious celebrations held in it. In 1805, the Brotherhood of San Rafael bought a small organ that soon proved insufficient to worship the Guardian of the city. Therefore, the brethren decided to undertake the construction of a first-class organ. The contract for its execution was signed in 1845, and it was inaugurated on May 6, 1848, on the eve of the celebration of the Archangel's last apparition. Made by Antonio Pilat, it is considered one of the great organs of the province of Córdoba. Joaquín Romero is the author of the case, and José González is the painter and gilder who polychromed it. Restored in 2015, it is used in the festivities of San Rafael and others held in the temple of the Oath.