An understanding of the structural complexity of mineralised tissues is fundamental for exploration into the field of diagenesis. Here we review aspects of current and past research on bone and tooth diagenesis using the most comprehensive collection of literature on diagenesis to date. Environmental factors such as soil pH, soil hydrology and ambient temperature, which influence the preservation of skeletal tissues are assessed, while the different diagenetic pathways such as microbial degradation, loss of organics, mineral changes, and DNA degradation are surveyed. Fluctuating water levels in and around the bone is the most harmful for preservation and lead to rapid skeletal destruction. Diagenetic mechanisms are found to work in conjunction with each other, altering the biogenic composition of skeletal material. This illustrates that researchers must examine multiple diagenetic pathways to fully understand the post-mortem interactions of archaeological skeletal material and the burial environment.