After the conquest of the city by the Catholic Monarchs, they ordered the consecration and blessing of the greatest mosque, devoting it to Saint Mary of the Incarnation.

In 1488, Cardinal Mendoza, through a bulla of the Pope Inocencio VII, proceed to the construction of the Malaguenian Cathedral. In that same year, Don Pedro Diaz de Toledo, first bishop of Málaga, published the bylaws of the church.

This same bishop command the opening of the Door of the Pardon, but it was not finished until the bishopric of Don Caesar Riario (1519-1540), according to the indications engraved in the shield built on it.

New altars and chapels were also erected, being that of Saint Gregory the only one conserving some Gothic remains.

As the temple was insufficient to cover the needs of the city, it was decided to build a new one. In 1528 being Don Bernardino de Contreras governing in behalf of the bishop Riario, it was decided to call the Toledian master Enrique Egeas and the stonecutter Pedro Lopez, so that they could revise and approve the plans.

It is not known who accomplished these plans and they were accredited to different persons; Egea, Siloé, Hernán Ruiz, or Juan Bautista de Toledo.

In the year 1588 the Cordovan, Hernán Ruiz III, and four years afterwards, the Sevillian great master, Juan de Minjares, supervised the Choir to which a new design was given, by Francisco de Mora, in 1598. Ended in 1631, it was demolished thereafter.

The works were stopped almost totally and not resumed until 1719. In 1782 were discontinued definitely, therefore, the south tower was never accomplished.