The Martrou Chapel was built in the Romanesque period. The presence of these different sanctuaries made Agen a stop on a pilgrimage route to Santiago de Compostela. A Martyr's Hospital[ was built next to the Martrou Chapel, which became its chapel, near the Saint-Caprais collegiate church. A Saint-Jacques Hospital was founded in the second half of the 14th century and not in the 12th century[. In 1562, the different hospitals of Agen, Saint-Antoine, Saint-Georges, Saint-Michel and Saint-Jacques, were united at the Martyr's Hospital[]. The whole was called the Saint-Jacques-du-Martyre Hospital. This hospital was closed in 1819 after its merger with the General Hospital for the Poor, which then took the name Saint-Jacques Hospital, before becoming the Hôtel du Département de Lot-et-Garonne in 1992.
The Martrou Chapel was part of the Saint-Caprais collegiate church. It currently belongs to the Sainte-Foy church. It has undergone numerous alterations, from the Romanesque period to the 20th century. It was restored after the merger of the various hospitals of Agen, after 1563. A room was built above the nave, which served as a meeting place for the Grey Penitents.
The choir fresco was painted in 1934 by Giovanni Masutti, an Italian-born painter who had worked in other churches in the department. The Diocesan Association of Agen undertook the renovation of the Martrou Church (enhancement of the bell tower, improvement of the acoustics, heating, paving of the crypt, restoration of the façade, painting of the choir, lighting, and whitewashing of the interior walls) in 2007. It was given a non-religious, but rather cultural, purpose.
The current chapel consists of a rectangular, paneled nave and a choir with a semi-domed vault. Below is a crypt built in the 4th century by the first Christians of Agen, on the site where the bodies of the first martyrs were buried.
The building was listed as a historic monument on November 29, 1995.