In 1763, the Oratory of San Felipe Neri had an organ built by Salvador Pabón y Valdés, very similar to the instrument in the church of Santos Justo y Pastor, since its design served as a model. This organ was destroyed during the French occupation at the beginning of the 19th century. Later abandoned after the disentailment process of 1836, the church was recovered in 1912 by the Redemptorist Fathers under the dedication of Nuestra Señora del Perpetuo Socorro. The current organ was assembled in 1913 by Pedro Ghys Guillemin, son of the Belgian organ builder Achilles Ghys, an official of Aristide Cavaillé-Coll workshop. Achilles Ghys settled in Granada after installing the Cavaillé-Coll organ in the Royal Chapel in 1888. The Perpetuo Socorro organ follows in its aesthetics the type of French romantic organ of the 19th century. It has 22 stops divided in two keyboards (Grand Orgue and Récit) and a 27 note pedalboard.

• Installed by Pedro Ghys Guillemin in 1913. 
• Restoration by Francisco Alonso in 2008.