Recent bioarchaeological analyses at the Neolithic Anatolian site of Çatalhöyük have revealed considerable variation in skeletal completeness, preservation, articulation, and flexion among burials. Furthermore, organic remains from burnt contexts demonstrate that many bodies were tightly bound and wrapped using cordage, matting, textile, and animal hides. Some of the observed variation is suggestive of a period of delay between death and final burial for certain individuals, likely as part of a multi-stage funerary rite, perhaps seasonal in nature. It appears that some bodies may have been processed in such a way as to facilitate their temporary storage prior to burial. We examined bone samples from 57 Çatalhöyük individuals using light microscopy and scanning electron microscopy (SEM) imaging techniques to determine whether specific funerary treatments can be associated with specific patterns of microstructural preservation. As endogenous gut bacteria released into the body at the onset of putrefaction are believed by some researchers to be responsible for particular patterns of microscopical focal destruction (MFD) observed in cortical bone, the lack of such bio-erosive features has been used to infer anthropogenic treatments aimed at reducing soft tissue body mass. A previous study of skeletal material from Çatalhöyük claimed to identify bacterial bioerosion in rib thin sections but did not make use of SEM. In the present study, our analyses reveal limited evidence for bacterial MFD, which highlights the fact that standard light microscopy is insufficient for properly documenting microbial bioerosion. While there is a range of variation among other taphonomic variables observed in the current study, it is difficult to associate this variability with specific human interventions. Furthermore, the complex role of local environmental and depositional factors must also be taken into account. As such, caution must be taken when using the presence/absence of bioerosion in human bone alone to assess ancient funerary practices.