The crypts of the Abbey indicate that it was originally a quarry during the Greek period and later became a necropolis from 2 BC onwards until Christian times. In 415, Christian monk and theologian John Cassian founded two monasteries at Marseille - the Abbey of Saint Victor for men and the Abbey of Saint Sauveur for women. However, both monasteries suffered from invasions by the Vikings and Saracens and were destroyed multiple times.
In 977, the monastic life was restored in the Abbey under the Rule of Saint Benedict through the efforts of Bishop Honorat and its first Benedictine abbot Saint Wiffred. From the middle of the 11th century, the abbots of Saint Victor were requested to restore religious life in the surrounding monasteries that had become decadent. Catalan monk Saint Isarn, who succeeded Wiffred as abbot, began construction work in 1020, building the first upper church, tower and altar. Isarn also played a vital role in obtaining the release of the monks of Lérins Abbey from Moorish captivity.
The Abbey of Saint Victor had contacts with the princes of Spain and Sardinia and even owned property in Syria. Its economic importance in the Middle Ages is documented in the polyptych of Saint Victor, compiled in 814, the large chartulary and the small chartulary. Blessed Bernard, abbot of Saint Victor, was one of the two ambassadors delegated by Pope Gregory VII to the Diet of Forchheim, where the German princes deposed Henry IV, Holy Roman Emperor. Gregory VII also sent him as a legate to Spain and in reward for his services exempted Saint Victor's from all jurisdiction other than that of the Holy See.
The history of the Abbey of Saint-Victor in Marseille dates back to the fifth century when a monastic community was established on the site. In the early fourteenth century, Blessed Guillaume Grimoard was made abbot of the abbey and later became Pope Urban V in 1362. During his tenure, he expanded the church, erected high walls around the abbey, and granted the abbot episcopal jurisdiction. He visited the abbey twice during his papacy, consecrating the high altar in 1365 and holding a consistory there in 1367.
Despite the abbey's flourishing during Urban V's papacy, it began to decline from the early sixteenth century, when commendatory abbots were appointed to manage the abbey's affairs. The decline was exacerbated by the loss of the abbey's valuable library, which was known to contain numerous ancient manuscripts. The library's contents were recorded in an inventory from the latter half of the twelfth century, but it was dispersed in the latter half of the sixteenth century, most likely during the tenure of Giuliano di Pierfrancesco de' Medici as abbot. It is believed that many of the books became the property of the king.
In 1648, the municipal magistrates of Marseille petitioned Pope Innocent X to secularize the monastery due to the monks' unsatisfactory behavior. Instead of granting their request, the Pope had the abbey taken over by the reformist Congregation of Saint Maur. However, the behavior of the monks did not improve, and after their poor response to the plague of 1720, Pope Benedict XIII secularized the monastery in 1726. It was converted into a collegiate church with a community of lay canons under an abbot, which was confirmed by a bull of Pope Clement XII in 1739.
In 1774, by royal decree, the abbey became a noble chapter whose members were required to be Provençals with four noble descents. They were granted the title of "chanoine comte de Saint-Victor." The last abbot of Saint-Victor was Prince Louis François Camille de Lorraine Lambesc, who died in 1787 and was not replaced before the French Revolution. The abbey's history reflects the changing fortunes of monasticism in France, as well as the complex relationships between the church and secular authorities during the medieval and early modern periods.
The abbey underwent significant changes in 1794 when its treasures were seized, with relics being burned, and gold and silver objects melted down to create coins. The building was then repurposed as a warehouse, prison, and barracks. The only remaining structure from the abbey is the church of St. Victor, which was originally dedicated by Pope Benedict IX in 1040 and rebuilt in 1200. The abbey was eventually restored and used for worship again during the First Empire and later in the 19th century. In 1934, Pope Pius XI declared the church a minor basilica.
Saint John Cassian's remains were once housed in the abbey's crypt, along with the remains of other notable figures such as Saints Maurice, Marcellinus, Peter, and Bishop Saint Maurontius. Additionally, some believe that the crypt also contains relics of the eponymous martyr of Marseille who lived during the 4th century.