Margat Castle, located on the eastern coast of Syria, is an outstanding example of architecture from the Crusader Period, and the most important castle of the Hospitallers, who were one of the most famous Christian military orders during the medieval period. Excavations by the Syro-Hungarian Archaeological Mission have been conducted with the aim of better understanding the history and material culture of this important part of Syrian heritage. Whilst large scale excavation and architectural analysis can provide an understanding of broad changes over the lifetime of the monument, high resolution studies of deposits are essential to understand their formation processes, and to test hypotheses suggested during excavation. In the refectory at Margat, a series of dark deposits overlain by a pale ‘ashy’ layer, were hypothesised to be the result of a large-scale burning event. In this study we aimed to test this hypothesis by conducting micromorphological and geochemical analysis of the sequence, the first application of microarchaeological techniques to medieval deposits in Syria. It was observed that the composition of the deposits relates to degradation of anthropogenic debris and constructional material through cycles of wetting/drying and microbial and faunal activity, rather than fire/destruction debris. These observations have clarified important changes in the castles' function associated with multiple phases of ownership.