Soil-borne plant pathogens are a major threat to the sustainable production of healthy crops and cost billions of euros annually. To reduce the environmental impact of pesticides and improve crop health, novel protection measures are needed. Our aim is to develop a novel method of crop protection that is sustainable and general. Specifically, we will use experimental evolution to evolve communities of beneficial root-associated bacteria that can be used to “vaccinate” soil to prevent soil-borne plant diseases. We build on the concept of “natural disease-suppressive soils”, defined as soils that eliminate or reduce specific diseases due to the concerted actions of root-associated microbes. Our novel approach will generate plant-beneficial microbiomes de novo using an experimental framework that can be applied to a broad range of soil-borne pathogens. We will provide proof-of-concept for a generic method to engineer beneficial soil microbiomes, thereby enhancing sustainable food production and safety. It will also serve as the impetus for Green Life Sciences and industry in the Netherlands and as the foundation for a larger national project to develop experimental evolution as an applied tool to evolve microbial communities for societally important functions.