The Royal Abbaye des Dames de Saint-Pierre owned the buildings until 1792. This 17th-century institution was frequented by high-ranking individuals in the French kingdom, as the abbess always came from the upper echelons of French nobility. The abbey was renovated during the 17th and 18th centuries by Louis XIV of France, giving it a particularly aristocratic character. These renovations, which included the construction of the baroque refectory and the monumental honour-staircase attributed to Thomas Blanchet, greatly contributed to the current state of the Palais Saint-Pierre. The refectory has been refurbished and now functions as a reception area for group visits, featuring two monumental paintings by Pierre-Louis Cretey on the theme of dining, The Multiplication of the Loaves and The Last Supper. Nicolas Bidaut and Simon Guillaume designed the remaining sculptures that make up the Palais Saint-Pierre's current layout.
During the French Revolution, the église Saint-Saturnin was destroyed, and the nuns were expelled, while the église Saint-Pierre, the abbey's other church, remained intact and currently displays sculptures from the 19th and 20th centuries. Following the Revolution, the remaining buildings were converted into the Palais du Commerce et des Arts, initially comprising works seized from the clergy and nobility but later incorporating collections from multiple disciplines, such as archaeology, natural history, and the Académie des Sciences et des Lettres. In 1805, the Palais du Commerce et des Arts established the imperial drawing school to provide silk factories in Lyon with designers, leading to the establishment of the renowned Lyon School. The Chambre de Commerce vacated the Palais Saint-Pierre in 1860, after which it was renamed the Palais des Arts. From 1875 onwards, the museum underwent a significant expansion, necessitating the addition of Pierre Puvis de Chavannes' staircase, which dates back to this period.
At the beginning of the 20th century, the collections of the Palais des Arts were significantly expanded, resulting in its transformation into the Musée des Beaux-Arts. In the mid-1990s, following the completion of multiple restoration projects, the building obtained its current layout.
The painting department houses a collection of European artwork spanning from the 14th century to the mid-20th century. The paintings are displayed chronologically and according to major schools, with a total of 35 rooms dedicated to this purpose. The collection includes notable works from:
The collection is divided into two sections. The ground floor houses Medieval and Renaissance sculptures and stuccos from the old baroque refectory, while the abbey's church displays sculptures from the 19th and early 20th centuries.
The former cloister, located at the heart of the abbey, has been transformed into a municipal garden that sits at the center of the town's peninsula. The garden is adorned with several 19th-century statues, including Auguste Rodin's "The Shadow" or "Adam" (1902) and "The Temptation of Saint Anthony" (1900); Léon-Alexandre Delhomme's sculpture of Democrites meditating on the seat of the soul (1864); Emile Antoine Bourdelle's sculpture of Carpeaux at work (1909); Aristide Maillol's Venus (1918–1928); James Pradier's Odalisque (1841), and Antoine Etex's group sculpture of Cain and His Race Cursed By God.
The antiquities department of the museum is centered around Ancient Egypt, which holds significant historical importance in Lyon, owing to the efforts of men like Victor Loret. In 1954, Loret's family donated over 1000 objects to the museum, and in 1895, the musée du Louvre contributed around 400 objects (such as unguent vases and funerary figurines) to establish the department. Additional items, including canopic vases, jewelry, and artifacts from Antinoöpolis, were later added to supplement this initial donation. The collection was further expanded in 1936 with objects from the artisans' village of Deir el-Medina.
The most prominent pieces in the collection are the sarcophagi and gates of Ptolemy III and Ptolemy IV from the temple of Medamud, excavated by the Lyon-based archaeologist Alexandre Varille in 1939 and donated by the French Institute of Oriental Archeology of Cairo. The remaining objects provide insight into daily life in Ancient Egypt.
In a single chamber, an assortment of relics from various ancient civilizations such as the Sumerian, Assyrian, and Babylonian are on display. Among them are cylinder seals, clay tablets, and bas-reliefs. Additionally, the room exhibits Luristan bronzes, ceramics, and statuettes from Cyprus, alongside a remarkable collection of Syrian artifacts that include an anthropoid sarcophagus and a marble bas-relief.
One room in this department is dedicated solely to the main attraction, which is the 6th century BC marble kore from the Acropolis of Athens. Another room is specifically dedicated to ancient Greece, housing a collection of Attic vases in black or red-figure, as well as bronzes and terracotta Tanagra figurines. Additionally, there is a small room dedicated to Magna Graecia, displaying various ceramics and bronze helmets.
The museum also features several rooms showcasing Roman sculpture, including marble statues such as the torso of Venus, a child riding a cockerel, and draped figures. There are also small bronze figurines depicting Gods from the Roman Pantheon like Mercury, Venus, and Mars.
Furthermore, the Gallo-Roman collections of Lyon, which were previously on display at the Museum of Fine Arts and the Antiquarium, were relocated in 1975 to the Lugdunum museum situated on the Fourvière hill near the Roman theatre and Odeon.
The "médaillier" of Lyon boasts an impressive collection of almost 50,000 coins, medals, seals, and other historical objects, making it the second largest in France after Paris. It has earned a reputation throughout Europe and has remained a significant player in the numismatic world since its inception in the 19th century, thanks in part to recent discoveries of valuable treasures such as those at Terreaux and Célestins.
At the dawn of the 19th century, a department was established to curate a collection of works on paper consisting of drawings, prints, engravings, watercolors, and the like, with an emphasis on line rather than color. The department boasts over 8,000 pieces, including masterworks by notable artists such as Filippino Lippi, Parmigianino, Fra Bartolomeo, Leonetto Cappiello, Nicolas Poussin, François Boucher, Ingres, Théodore Géricault, Eugène Delacroix, Camille Corot, Honoré Daumier, Odilon Redon, Puvis de Chavannes, Edgar Degas, Henri Matisse, Fernand Léger, and a particularly noteworthy study by Albrecht Dürer.