Evidence has accumulated supporting the beneficial impacts of strategically diversified cropping systems on ecosystem services like plant resistance to herbivory, but the underlying mechanisms remain largely unknown. Through a microcosm experiment we investigate how intercropping and cover cropping with three different companion legume species change plant secondary metabolite profiles of focal maize plants, the resulting effects on herbivore resistance, and the potential for such ecosystem services to persist when using a conventional maize variety. Intercropping produced a fundamentally different leaf and root secondary metabolite profile compared to maize plants grown under cover crop-conditioned soils. In leaf and root tissue, defense-related compounds such as benzoxazinoids were upregulated under intercropping, affecting maize metabolic profiles in a companion species-specific manner. Resistance bioassays to the generalist herbivore Spodoptera frugiperda revealed that intercropping significantly reduces the overall leaf area consumed, while bean intercropping increases larval mortality and alfalfa intercropping reduces larval mortality. Our results contribute to the understanding of diversified cropping systems by studying how plant-plant and plant-soil interactions drive metabolic changes leading to different resistance outcomes and show how these positive resistance effects persist under conventional systems. These insights are crucial to inform adoption and development of synergistic relations in diversified agricultural landscapes.