Tomatoes are globally recognized as an important crop due to their sensory properties and abundant bioactive compounds. However, their susceptibility to contamination by fungus and other pest, has resulted in an increase in pesticide use for crop management. Pesticide can remain in fruits and their products, reducing their functionality. In this review, we discussed the profile of bioactive compounds related to defense mechanisms of tomatoes that could be stimulated in the crop as a friendly strategy to mitigate the risk of fungal and mycotoxin contamination. The beneficial effects of genetic modification and plant management to improve resistance to biotic and abiotic stress have been highlighted in several publications. The effect of crop management on the profile of phenolic compounds, minerals, elicitors, phytoalexins, defense enzymes and amino acids in tomatoes and other fruits was also demonstrated. However, the challenge of developing a model to demonstrate the interaction of these abiotic parameters and vegetable resilience remains, since there are several multivariate relations between defense mechanisms and the fungal susceptibility of tomatoes. The review will be useful to researchers engaged in promoting safer and more sustainable techniques to mitigate fungal contamination in tomato crops. • Tomatoes are rich in compounds which participate in their defense mechanism. • Micotoxicologic contamination is prevalent in tomatoes. • There are friendly strategies to decrease the risk of fungal contamination.