Evolutionary biologists have recently solicited archaeologists to help document and understand the morphological evolution of animals in response to human activities and, more globally, to help reconstruct the history and significance of the anthropogenic impact on worldwide ecosystems. Artificial selection associated with domestication is the best-known example of a major anthropogenic morphological evolution preserved in the archaeological record. However, the impact of the domestication process and dispersal on the morphological evolution of animals has been far less explored. To fill this gap, we focused on 5,000 years of Neolithic transition in Western Europe – a major anthropogenic ecological disturbance involving landscape modification and the translocation of domestic mammals. Using geometric morphometrics on key phenotypic markers preserved in the archaeological record associated with isotopic studies, we explored how and according to which cultural drivers the Neolithic niche construction has influenced the morphological evolution of wild boars (Sus scrofa). The decoupling of size and shape components from bone morphological variation has facilitated the identification of several processes of phenotypic diversification of Sus scrofa in response to human behaviour during the Neolithic transition in Western Europe.