Discussions of heat treatment in the southern African Middle Stone Age often focus on the importance of this innovation to the development of complex technologies and the evolution of modern human cognition. Debates regarding the context of silcrete heat treatment typically include the amount of time and resource investment needed, and when the earliest occurrences of heat treatment appear in the archaeological record. However, silcrete is a heterogeneous material and the potential effects of this heterogeneity on the thermal transformations that occur during heat treatment are not well established. We undertook a series of controlled experiments using direct transmission near-infrared spectroscopy on South African silcretes from multiple sources heated to a range of maximum temperatures to examine the degree of heterogeneity in starting structural content and the evolution of thermal transformations. We found that material source is an important determinant of starting concentrations of H2O, SiOH, and pore space in silcrete, as well as the thermal evolution of these variables. These results shed light on the degree and sources of variation in the structural content and thermal behavior of silcrete during heat treatment and allow for a better understanding of the heterogeneity of silcrete as a raw material and the implications of this for African Middle Stone Age pyrotechnology.