At Liang Bua (Flores, Indonesia), the transition from the Homo floresiensis layers to the modern human layers ~50–46 ka is accompanied by a remarkable shift in lithic raw material usage. Prior to 50 ka, the H. floresiensis lithic assemblages are consistently dominated by artefacts made from silicified tuff, whereas the use of chert remained relatively low. In comparison, the proportion of silicified tuff artefacts decreased notably after 46 ka among the modern human assemblages, while that of chert artefacts increased considerably. In this paper, we report the results of a detailed analysis of the silicified tuff and chert represented at Liang Bua, both of which are available in the site vicinity today. We show that the two stone types are mineralogically alike, both derive from fossiliferous limestone that had undergone diagenetic silica replacement. Mechanical testing indicates that the ‘chert’ is harder than the ‘silicified tuff’, but the influence of this hardness difference on the knapability and functional performance of the two raw materials may be limited. Alternatively, we use a simple model to show that the changing raw material usage pattern at Liang Bua can be explained by a shift in hominin mobility and land use. Specifically, the rise in the proportion of chert artefacts post-46 ka can be a result of the modern humans practicing a more expansive foraging range than the H. floresiensis. Our findings suggest that variation in hominin behaviour at Liang Bua, and perhaps across Southeast Asia in general, may not necessarily be expressed in the form and production of stone artefacts, but rather through broader processes of land use, social network and technological organisation.