The organ of the Convent founded in 1520 by the widow of Hernando de Zafra is the work of the same organ builder of the Monastery of San Jerónimo, the Franciscan friar Francisco Alexo Muñoz. It is one of the most beautiful baroque organs in Granada, which dates back to 1730. It is placed in the traditional Spanish manner on one side of the nave, next to the choir, with the peculiarity of some conventual organs in which the keyboard is located at the back of the organ, in order to preserve the conventual enclosure. Although it appears to be modest in size, it actually has two keyboards and a large palette of sounds and possibilities.

• 1730: built by Fray Francisco Alexo Muñoz
• 1780: intervention by Fray Pedro de San Miguel
• 1846: intervention by Juan Quesada
• 1882: itervention by Miguel Rivero
• 2004: restoration by Francisco Alonso Suárez

Two keyboards (Órgano mayor and Cadereta interior) of 45 keys (C-c3). Short octave. Divided stops between c1 and c#1.