The shift towards cultivating domesticated crops was a pivotal development in ecological, economic, and human behavioural systems. As agriculture expanded beyond its origins, it faced diverse environments, often unsuitable for the originally cultivated domesticates. Farmers in Central Europe had to adjust and transform their farming systems, typically cultivating only five domesticated crop species. Here, we present new archaeobotanical data comprising 7955 determined charred remains and 22 radiocarbon dates from South Bohemia. This region, with higher altitudes, colder climates, and less fertile soils, lies on the periphery of Early Neolithic settlement. Our results reveal increased crop diversity as a form of adaptation to the harsher environment that bolstered resilience against crop failure. The earliest 14C-based evidence of deliberate cultivation of barley and Timopheev’s wheat in the region also provides new insights into the interplay between crop diffusion, landscapes, and food choices in the Neolithic Central Europe.