Rooms 5 and 6 show sculptures made by Master Bartholomew, marking the transition between Romanesque and Gothic. They are clear examples of the grouping by Calvari in the 13th century, from Girona Cathedral, along with the tympanum at the clergy hospital in Girona, recently restored. In the 14th century there was also room for more delicate sculptures influenced by international Gothic trends, such as the work of Master Aloi or Jaume Cascalls. Some of the most important pieces in the collection, located in Room 7, are the stained glass window tables that were used to make the windows in the apse in Girona Cathedral, as they are some of the few surviving examples in Europe of the tools used to make a stained glass window.
The majestic Throne Room, in Room 8, includes a collection of some remarkable altarpieces from the 15th century, including works from the Sant Miquel de Cruïlles monastery by Lluís Borrassà, "Mare de Déu de la Llet" from the Sant Esteve de Canapost church, the altarpiece from Sant Miquel de Castelló d'Empúries church and the altar the Sant Pere de Púbol church. All of these pieces are by artists who worked in the Girona region during the 14th and 15th centuries.