In on-farm comparisons throughout Ohio and greenhouse studies, we have confirmed anecdotal reports by farmers that plants growing in organically managed soils are often more resistant to insects and disease than those grown in conventionally managed soils. We applied recently developed tools of functional genomics and metabolomics to elucidate the mechanisms underlying a soil-based resistance of tomato plants to insects and diseases. Microarray analysis showed consistent differences in RNA expression between plants amended with compost versus chemical fertilizer. Likewise, soil amendments led to significantly different profiles of sap amino acids and sugars, which strongly impact insect and disease development.