There is an urgent need of alternative strategies to control postharvest diseases and mycotoxins contamination of fruits and vegetables, because of the progressive reduction of conventional means and the high economic losses. In this study, a multiplex qPCR assay was designed on pksI and idh, key genes of alternariol and patulin biosynthesis, respectively, to detect toxigenic strains of Alternaria alternata and Penicillium expansum. The assay was specific and sensitive, with a detection limit of 1 pg. Furthermore, two alternative means, namely electrolyzed water and active coating, were applied against postharvest rots. The results indicated that the electrolyzed water, obtained using sodium chloride as electrolyte, completely prevented fungal growth in vitro while decreasing disease severity by 70 to 100% in vivo. Furthermore, the sodium alginate-calcium chloride edible coating, containing Moringa oleifera leaf extract or sodium bicarbonate as active ingredients, reduced the susceptibility of cherry tomatoes and strawberries to A. alternata and B. cinerea. The proposed comprehensive approach seems promising as alternative control strategy to postharvest losses and wastes of fresh fruits and vegetables.