The Gothic upper chapel was build at the end of the 15th century. Only the curved arches giving access to the sidechapel of the Holy Cross are the remains of the original Romanesque chapel. The stained-glass windows in the choir are dated 1845 and represent the sovereigns who reigned over the County of Flanders from Philip the Bold, duke of Burgundy (1342-1404), till Maria-Theresia, empress of Austria (1717-1780).

On both sides of the high altar one can see decorations typical to a basilica : the tintinnabulum, a small processional bell, and the conopeum, a sunscreen in the form of a parasol in yellow and red silk. The pulpit made by Henry Pulinckx in the form of a globe dates from 1728. The reason for this shape can be found in its evangelical purpose : " Go into all the world and preach the gospel ".

The large wall-painting behind the altar was realized in 1905. The upper part depicts the mystery of the Cross, where Christ shed his blood. In the background can be seen the towns of Bethlehem, where Christ was born, and Jerusalem where he died.

The fresco underneath shows the transport of the relic to Bruges : on the left, Thierry of Alsace receives the relic from the Patriarch and King of Jerusalem ; on the right, kneeling besides Countess Sybilla, he hands over the relic to the chaplain.

The altar used today for the Eucharist is decorated with a relief in alabaster dating back to the beginning of the 17th century and depicting the Last Supper. The oak communion rails (17th century) bear four carved medaillons of saints.

The white marble altar in Baroque style in the chapel of the Holy Cross was completed in 1751 by Laurent Delvaux. The two adoring angels were made by Peter Pepers and the silver tabernacle by silversmith Ryelandt. To the right of the altar there is an impressive painting by Jacob van Oost, depicting the descent from the Cross.