Feeding a growing population and ensuring food security whilst protecting ecosystems and natural resources are crucial priorities in times of global changes. Agroecology promotes innovative drivers of change for a smart agriculture that meets the specifications of ecological transition. Managing soil interactions offer largely unexplored potential to increase agricultural yields and reduce pressures on the environment. Crop losses of 10 % are due to soil-borne pests causing root rot, root blackening, wilt, stunting or seedling damping-off. One promising approach is to encourage pest regulation provided by soil interactions to decrease the inputs of pesticides. However, limited success of this approach in field applications raises questions as to how this might be best accomplished. Here we review advances in plant protection against soil-borne pests and implications for disease-suppressive agrosystems design. Root infection processes are increasingly understood. Plants protect themselves by naturally engineering the composition of their rhizosphere. They fight soil pests both by root production of toxic chemicals and by favoring pest enemies. The analysis of the chemical dialogue offers new perspectives to enhance biocontrol effectiveness of disease-suppressive soils and antagonists. High throughput technologies provide unprecedented knowledge on rhizosphere interactions and implications for crop health. Agroecological engineering approaches overcome the limitations of conventional protection strategies by promoting multi-functional practices harnessing rhizosphere bioprotection. Breeding crop cultivars which capitalize on plant-microbiome interactions or associating plants and biocontrol agents early in their life offers innovative ways to contribute to disease-suppressive agroecosystems design. Integrating interacting species with strong ability to recruit beneficial microorganisms or secrete toxic compounds in mixed cropping systems is a key issue. Based on functional biodiversity management, these systems will provide underpinning ecosystem services and enhance global resiliency of agroecosystems.