Tortoises are one of the most common faunal components at many Palaeolithic archaeological sites across the Old World. They provide protein, fat, and other ‘animal’ resources in a ‘collectable’ package. However, for most sites their interpretation as human food debris is based only on association, rather than demonstrated through taphonomic analysis. Because of their very different anatomical configuration compared to mammals, it is difficult to conduct such analyses by directly applying the taphonomic methods used to interpret large mammal assemblages. Tortoise-specific taphonomic analysis is presented here for the Still Bay layers at the important Middle Stone Age (MSA) site of Blombos Cave (BBC), Western Cape, South Africa. Research on MSA subsistence systems at sites such as BBC has almost exclusively relied on analysis of large ungulate remains, in spite of the fact that many of these key sites contain equal or greater numbers of tortoise fragments. In this analysis we show that human modification is common on the BBC tortoises, and that there are consistent patterns of fragmentation and burning that indicate set processing sequences including cooking while in the shell, hammerstone percussion, and human chewing of limbs. The almost exclusive dominance of the angulate tortoise, Chersina angulata, is confirmed by full skeletal element analyses rather than only counts of single elements such as humeri. The sex distribution can be reconstructed for this species, and is female-biased. For all tortoise assemblages, taxonomic and skeletal element abundance data should be calculated from a sample of complete elements, or at minimum the entoplastron and humerus. A sample of shell and limb/girdle elements should also be subjected to microscopic bone surface modification analysis, as modifications are often rare or subtle but highly informative. Using this approach, analysis of breakage patterns, bone surface modification, and burning patterns can be understood together to specifically reconstruct tortoise collection, processing, and human dietary significance across a range of archaeological sites.