The site was initially occupied in the twelfth century by a hospice and chapel of the Knights Hospitaller of the Order of Malta, under the jurisdiction of the priory of Saint-Gilles in Provence. The thirteenth-century church formed part of a priory of the same order situated in olive groves outside the city walls of Aix. From the thirteenth century it served as a burial place for the Counts of Provence. In the 17th century the parish was incorporated within the city of Aix when the ramparts were extended to the south and the adjoining lands of the priory sold off to help create the quartier Mazarin. In the aftermath of the French revolution most of the internal furnishings, treasures and statuary of the church were removed or plundered and the church itself converted into a military storehouse. In the 19th century it was eventually restored to religious use as a parish church. The church is currently under the ministry of a brotherhood of apostolic monks. The nineteenth century organ in Saint-Jean-de-Malte was replaced in 2006 by a baroque-style organ built by Daniel Kern. The interior of the church may be seen in Michelangelo Antonioni's 1995 filmBeyond the Clouds.
Windows and stained glass
The reopening in 1858 of the large window in the apse, blocked by Jean-Claude Viany for the installation of a large altarpiece in the seventeenth century, revealed traces of polychrome stained glass indicating that in the seventeenth century the church not only had monochrome grisailles but also coloured windows, with at least some of them depicting Saint-Jean-de-Malte himself. The windows in the church today date from the nineteenth and twentieth centuries. The new window in the apse was completed in 1858 and was designed by several artists from Aix. In the upper quatrefoils are God the Father, crowned with a globe in his left hand as he delivers a blessing with his right hand. He is flanked by Ramon Berenguer IV, Count of Provence and Beatrice of Provence. In three smaller quatrefoils below are three knights hospitaller of Malta: Berenger Monachi, Gerard Thom and Hélion de Villeneuve. The three pairs of windows below represent scenes from the life of John the Baptist: his meeting with the Virgin Mary; the baptism of Christ; and with Christ in a diptych. In the six panels below are Old Testament figures : Abraham, Moses, Isaiah, Jeremiah, Ezekiel and Daniel. At the base of the window are six thirteenth century coats of arms connected with the Order, including those of Provence, Malta, Aragon and Aix. Other notable windows include the large rose window above the entrance to the church installed in 1896: the original rose window was blocked by Viany in the seventeenth century to make room for an organ. In 1984 an abstract window by Henri Guérin was installed in the southern transept. Its coloured blocks were designed to take advantage of the changing quality of sunlight at different times of day and liturgical season.
Paintings
Although in the seventeenth century the prior Jean-Claude Viany commissioned paintings from Gilles Garcin and sculpture from Christophe Veyrier and his nephew Thomas, some of which can be still be seen in the church, the lack of funds when the parish was re-established after the French revolution limited the further acquisition of paintings. A number of paintings, however, have come from disestablished churches or have been donated privately, including most recently the Crucifixion by Delacroix.
St Henry pleading with the Virgin for the souls in purgatory, Jean Armelin
The Annunciation and Death of the Virgin, André Boisson
