Despite its harsh and arid conditions, the Gobi Desert has played an important role in shaping Holocene populations, including the transition from hunting to herding lifeways. Here we present three newly documented rock art sites in the Gobi-Altai Mountains of south-central Mongolia, a cave (Gazar Agui 1), a rock shelter (Gazar Agui 13) and an open-air landscape site overlooking a palaeolake (Unegt Uul). In addition, we re-examine the preservation of the rock art cave site of Saalit Agui some 20 years after its original documentation, using digital technology not available at that time. Comparisons of rock art at Gazar Agui 1 and Saalit Agui with previously documented rock art in Mongolia suggest links with Mesolithic and Neolithic anthropomorphic iconography. Unegt Uul and Gazar Agui 13 show Early Bronze Age to Iron Age symbols, suggesting two distinct periods of production, by hunter-gatherers during the Early Holocene and by later hunter-pastoralists during the Late Holocene. Our findings suggest that wet periods in mountainous basins of the Gobi-Altai were likely key to early human habitation, with pastoralism dominating during arid periods. Our observations further indicate that preservation of rock art sites in the region is currently under threat due to human activity and climate change.