These files contain data and scripts supporting all results reported in Jordán & Kessler, Journal of Applied Ecology, Intercropping and cover cropping differentially alter maize secondary metabolism and affect herbivore resistance, 2025. In Jordán & Kessler, 2025 we found that the non-volatile secondary metabolite profiles of maize leaves and roots differed across inter and cover cropping systems, while volatile organic compound emissions remained largely unchanged. Defense-related compounds such as benzoxazinoids were generally upregulated under intercropping, while the companion plant identity further shaped the maize defense profile with bean-intercropping specifically upregulating benzoxazinoid compounds. Resistance bioassays with the generalist herbivore Spodoptera frugiperda revealed that intercropping significantly reduces leaf damage relative to cover cropping. Among the intercrops, beans increase larval mortality while alfalfa decreases larval mortality on maize plants.