The transition to agriculture was a key event in human history. The extent to which this transition is associated with biological changes in different world regions remains debated. Cultural and osteological records in Lower Nubia throughout the Holocene have been interpreted as a result of in situ differentiation or alternatively as migratory events and possible admixture with surrounding populations. Here we investigated the patterns of craniofacial and mandibular variation from Mesolithic hunting-gathering to late farming, a period spanning 11,000 years. We analyzed 102 adult specimens spanning five cultural horizons: Mesolithic, A-group, C-group, Pharaonic and Meroitic, by means of 3D geometric morphometric methods, in order to assess shape variation and diachronic patterns at the transition to farming and in subsequent periods. Our results highlight a strong morphometric distinction between Mesolithic hunter-gatherers and farmers as well as differences between transitional and intensive farmers in mandibular variation which is consistent with differential impact of selective pressures on different regions of the skull. This study corroborates a major biological change during the transition from hunting to farming, supporting the masticatory-functional hypothesis for the mandible and suggesting population continuity among farming populations throughout the Holocene based on the overall shape of the cranium.