The study, by researchers from the University of Barcelona and Spain's Institute of Health, was reported in The Journal of Agricultural and Food Chemistry.
The researchers suggested that higher levels of a number of polyphenols were due to organic fruit taking longer to ripen and being grown in less nutrient-rich soil.
However the government's NHS Choices website said that the results did not necessarily show organic tomatoes to be healthier, as evidence on the effects of antioxidants on the body was contradictory, adding:
"This research tells us more about the effect of farming techniques on a tomato’s nutrient content than it tells us about the effect of a tomato’s nutrient content on our health. However, the field is ripe for someone to conduct controlled trials looking at health outcomes for people."