Disease and pest management in organic agriculture are based on a whole set of interlinked system management methods, including in certain cases, the use of organic pesticides and biocontrol organisms. In order to achieve the greatest possible natural biological control within a growing system, there is a need to apply a holistic biological systems management approach. Two case studies working towards these aims are presented in detail: a systems approach aiming at a soil regenerative potato cropping system (RePCRO) and evolutionary breeding for diversity in wheat. Both systems greatly increase overall resilience to unpredictable biotic and abiotic environmental challenges. We conclude that soil quality and health on the one hand and biodiversity on the other hand are inseparably connected to plant health management in organic agriculture. Addressing the whole production system starting with breeding for diversity and soil management for enhanced soil health will result in innovative plant health management options within highly resilient and sustainable agricultural systems.