When the Crusaders arrived in Jerusalem they found in ruins the area of Sion where only the two storey chapel of the Cenacle had survived. It is here that Raymond of Tolouse put camp to protect the area from the intruding enemy. It is here too that Patriarch Daibert lived for some time before the coronation of Baldwin I.

The Crusaders raised on the ruins of the old church a monument worthy of the title Mater omnium Ecclesiarum. The edifice was divided into three naves. In the northern nave stood an edicule in memory of the Dormition of the Virgin. In the southwest angle of the centre nave arose the Cenacle composed of two superimposed chapels and divided in the centre in such a way as to form as it were four chapels, two below and two above. Thirty steps led up from the lower to the „Upper” room, where the Institution of the Eucharist and the Descent of the Holy Ghost were represented in mosaic.
The lower chapel, called the Galilee, recorded the washing of the feet and the Apparition of the Risen Christ to the Apostles. The basilica was served by the Canons Regular of St. Augustine. It is interesting that during the Crusader period no pilgrim mentioned the tomb of David. Only in 1167 Rabbi Abraham of Jerusalem told the pilgrim Benjamin of Tudela that 16 years before, following the collapse of a wall, rich tombs believed to be those of David and Solomon were discovered. The Latin Patriarch had called this Rabbi Abraham from Constantinople to examine the two witnesses who had found the Tombs. When these two, who had barely escaped with their lives, refused to return, the Patriarch had the place closed up. This story probably has its foundation in the legend of Josephus Flavius regarding Herod and David’s tomb: „However, he had a great desire to make a more diligent search, and to go farther in, even as far as the very bodies of David and Solomon; where two of his guards were slain, by a flame that burst out upon those that went in, as the report was” (Antiq. XVI 7,1).

From this it would seem that the local people still held to the legend that David was buried there. When Saladin captured Jerusalem in 1187, the basilica of Sion was one of the few churches that was not destroyed or turned into a mosque. It was given into the care of the local clergy, Syrians. During this period the western pilgrims were permitted to visit the Cenacle and priests allowed to celebrate the Eucharist. In 1192 the Basilica and the monastery were enclosed by walls, but in 1219 by order of Malek el Muadden the place was in part destroyed, and later destroyed completely by the Khwarismians in 1244. The Greek pilgrim, Perdiccas, in 1260, speaks of the tomb of David in the lower chapel. By 1294 the Dominican Ricold da Montecroce saw the building already in ruins, part of it a mosque.

To understand later pilgrims it is necessary to remember that the name Cenacle was reserved to the western section, where the Institution of the Eucharist was commemorated. When the building had collapsed into ruins, it would seem that this particular part remained standing, as it is mentioned by all the pilgrims as the only thing standing in the ruins of Sion. Many pilgrims of the first quarter of the 14th century describe the Sanctuary and all give the same account.