Plants are the ultimate source of nutrients in the human diet. To ensure adequate availability of high quality food for an increasing world population, traits including improved tolerance of stresses and nutrient levels need to be selected in crops, both individually and in combination. Here we report the identification of SlMX1 encoding a MIXTA-like MYB transcription factor in tomato that simultaneously modulates drought resistance and metabolic processes through regulating key structural and regulatory genes of the corresponding pathways. Over-expression of SlMX1 results in substantially increased drought tolerance and improved fruit quality, while knocking down SlMX1 resulted in the opposite phenotypes. Our study indicates an effective way with multiple beneficial traits by genetic engineering of a single regulatory gene and can be a novel approach to breeding crops.