The tesserae for the church mosaic had to be cut and set in place one at a time. The restorers brought stones from all over Israel to match the various colors of the original and then handcut the stone into the tiny tesserae. They ultimately purchased an electric saw to cut the two million pieces that were needed, but the reconstruction of the mosaic was still done carefully by hand, using cement and other materials similar to those used in the Byzantine period.

After the successful completion of the church floor, excavator Yitzhak Magen and others decided to use the newly acquired skills of the mosaic team to create a mosaic museum at the site. Damaged mosaics were brought from across the land to the museum for preservation and display. First, broad strips of cloth were glued to the tops of the patterned mosaics to preserve the designs. Section by section they were then laid in place (cloth side up) on a bed of plaster, where they would be displayed. After the mosaic was set, the cloth was slowly removed to reveal the tesserae. Workers also restored damaged or missing portions of the mosaics brought to the site.