Karst-derived breccia is the most analysed deposit in fossil-bearing Southeast Asian caves due to its superior preservation potential for human, faunal, archaeological, and palaeontological data. The study of breccia can provide a better understanding of human and faunal histories, and an opportunity to investigate site taphonomy and insights into environments of deposition and post-depositional processes. We review the literature on approaches used to improve the taphonomic understanding of cave deposits in Southeast Asia and how these deposits fit into a cave’s life history. We discuss common methods used to extract taphonomic data retained in Southeast Asian cave deposits and the associated opportunities to discern the mechanisms of cave formation, depositional history, and faunal accumulation. While attempts have previously been made to discern the taphonomic characteristics of Pleistocene vertebrate remains in the region, there has been no comprehensive review outlining methods used to understand taphonomic histories and the biases introduced through these processes. We illustrate the challenges of researching cave breccias in Southeast Asia and the knowledge gaps brought about by conventional methodologies. Uncertainties exist about the extent to which breccia can be examined to infer the taphonomic history of a vertebrate assemblage. These uncertainties exist in part because of dating complexities. This review demonstrates that a taphonomic analysis of breccia in complex long-term accumulations requires a multi-disciplinary approach. We recommend using digital techniques to record spatial distribution data for a thorough interpretation of taphonomic characteristics.