Holocene environmental dynamics and the onset of early subsistence farming during the Neolithic period have led to major surface modification and landscape transformation in the Carpathian Basin. In this context, Neolithic settlements and agricultural activities were supposed to be located on Chernozem soil patches, which originated from loess-covered surfaces of the uneroded Pleistocene and early Holocene palaeolevees. Chernozem soil distribution is seen as an important precondition of agricultural expansion. However, Chernozem soil genesis and the anthropogenic modification of soil organic matter and Black Carbon (BC) content from clearing and vegetation burning are not yet fully understood and there is increasing evidence for the active role of human landscape interaction in the process of Chernozem development. Consequently, Neolithic land-use would not have been necessarily linked to Chernozem but rather triggered its development from alluvial and meadow soils through intensified surface transformation. This article applies a GIS-based multivariate surface analysis and a statistical evaluation to 49 Neolithic sites to track environmental location factors, soil preferences, and potential land-use strategies in Neolithic Hungary. The combination of remotely sensed surface data, environmental GIS-attributes, quantitative statistics, and archaeological datasets reveals site-location parameters during the Early to the Late Neolithic and critically discusses Chernozem soil development and utilization during agricultural transformations across Europe.