Aspergillus flavus affects fresh and dry fruit and vegetable products, and its toxic metabolites, namely aflatoxins, cause serious damage in humans. The objective of this research study was to evaluate the effect of commercial natural products as well as edible and nanostructured chitosan coatings on the development of A. flavus and on the production of aflatoxins in vitro and in tomato. Treatments were as follows: chitosan 1%, chitosan coating, chitosan nanostructured coating, Citrocover 1% (citrus seed extract), Resinadher 0.5% (pine resin extract), mancozeb 2%, and water. The variables were as follows: halo inhibition, spore production, and aflatoxins content. In fruit, the following were evaluated: disease incidence, mycelial growth, and aflatoxin production. An ANOVA (Tukey: p < 0.05) was used. In vitro results showed that Citrocover and Resinadher reduced sporulation (0.2 and 0.9 × 105 spores mL−1, respectively), while chitosan inhibited the production of aflatoxins. With Resinadher and Citrocover, tomato fruit had the lowest incidence, mycelial growth, and aflatoxin production with corresponding values of 0%, 0.0 cm2, and 0.95 ppb, respectively, and 7%, 0.2 cm2, and 1.77 ppb, respectively. The use of Citrocover and Resinadher could be a viable alternative to decrease the development of A. flavus in tomato fruit.