This paper is the first to use an innovative multi-proxy approach to obtain insights into hitherto unknown Mithraic cult practices. Using soil micromorphology, zooarchaeology and histotaphonomy, we investigated two mithraea (Biesheim FR, Kempraten CH) and one cult cave (Zillis CH). This was also the first study to include micromorphological and histotaphonomic approaches within the context of Mithraic research. The systematic evaluation of thermal alteration and bioerosion (in particular bacterial attack) on the animal bones, in combination with zooarchaeological results, allows a differentiation between various (cult) practices involving animals. Thanks to the micromorphological investigations, it was possible to demonstrate that repeatedly spreading combustion residues and renewing the floor were important parts of the cult practices of Mithraism. Our results suggest that a cult practice consisting of several stages was carried out on all three sites. Our study highlights that multiple floor constructions as well as the related sediments and (micro-) artefacts of cultic indoor features are important sources of information.