As far as the exterior of the basilica is concerned, the Early Modern period brought no changes with it, except for the demolition of the Valois mausoleum, which had to be removed because it threatened the stability of the church.

The medieval monastery on the other hand, was subjected to an ambitious reconstruction program that, for a short time, left only the treasury building untouched. The layout of the reconstructed monastery took the form of a large square around a cloister with two right-angle wings to the south. In the corners formed by these wings, two buildings housed, respectively, the kitchens to the west and a large staircase to the east. The center of the western facade featured a polygonal salient, covered with a domed roof. The external appearance of the monastery in the eighteenth century has remained unchanged to the present day. Modifications were carried out following the building being given over to the Maison d'éducation de la Légion d'honneur. These include the removal of a building facing the church that housed the night staircase for the dormitories on the upper floor as well as a covered passageway that provided a direct link between the northern aisle of the cloisters and the monks' choir.

North of the basilica, the Saint-Pierre, Saint-Michel-du-Charnier and Madeleine churches remained as they were. Further to the west, the Saint-Michel-du-Degré and Sainte-Geneviève churches were rebuilt in the form of a new church, known as the Trois-Patrons church. Since a section of the apse and a part of the north wall of this structure are still visible-now part of the administrative building of the town hall-it is relatively simple to reconstruct this church, which had a single nave opening to the east on a semicircular choir that had the same width. The structure, which was seven bays long, allowed for the porch-bell tower of the Sainte-Geneviève church to remain as part of its west face.

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