In early Christian society, the continuation of pagan beliefs and apotropaic elements derived from the Roman culture can be observed in the reflections of artistic production. Apotropaic themes bearing the traces of paganism, such as the Medusa head and the mask were used continuously for decorative purposes by Christian artists. These motifs also show apotropaic features aligning with the Christian faith in the decoration of the new Byzantine art. We can see that the majority of artists who drew the wall paintings in the region were local artists socialized within Hellenistic traditions and with Christian knowledge. While painting the motifs with sacred meanings and apotropaic effects in the church, Byzantine artists focused on the harmony of these motifs with the Byzantine aesthetic. In this sense, it should not be forgotten how effective it is from a viewer’s point of view to add a sacred meaning and apotropaic effects to these motifs in the Cappadocian wall paintings in the mid or late Byzantine era. In our study, we will emphasize the motifs we have encountered in the wall paintings of churches, especially in the Cappadocia region, dating back to the middle and late Byzantine periods, such as leaf mask, moon, sun, eight-pointed rosette, rotating disk and medallion, guilloche, interlace, zigzag, three-dimensional folded plate, precious stones and their location within the church, their use of color, and their sacred apotropaic meaning. Moreover, an evaluation of the effects of the doctrines of Cappadocian church fathers on this situation in Byzantine art, especially about the manuscripts and wall paintings of the period, will be conducted by comparing the art within the material historical framework.