The shelf-life of tomato (Solanum lycopersicum) fruit is determined by the processes of over-ripening and susceptibility to pathogens. Post-harvest shelf life is one of the most important traits for commercially grown tomatoes. We compared the shelf life of tomato fruit that accumulate different flavonoids and found that delayed over-ripening is associated with increased total antioxidant capacity caused by the accumulation of flavonoids in the fruit. However, reduced susceptibility to Botrytis cinerea, a major post-harvest fungal pathogen of tomato, is conferred by specific flavonoids only. We demonstrate an association between flavonoid structure, selective scavenging ability for different free radicals and reduced susceptibility to B. cinerea. Our study provides mechanistic insight into how flavonoids influence shelf life of tomato, information which could be used to improve the shelf life of tomato, and potentially of other soft fruit.