Abstract Molds and their toxins, mycotoxins, are of major global challenges in the food industry due to their harmful effects on human health as well as their economic losses. Tomato and its products are prone to fungal spoilage at industrial and consumer levels. In this study, we aim to emphasize the presence and significance of mycotoxins not only in spoiled tomato-based products but also in the products without visible growth of fungi. According to our systematic review, main mycotoxins in tomatoes and their derivatives are Alternariol (AOH), Alternariol methyl ether (AME), Tenuazonic acid (TeA), and Patulin (PAT). Among them, TeA has the highest concentration in tomato-based products. Thus, it should be deemed as a health risk. We also outlined some of the current and potential antimicrobial techniques and their inhibitory effects on mycotoxins in tomato and derived products. Finally, we emphasize the need for further studies on the health risk assessment of most concerning mycotoxins (TeA and AOH) in tomato-derived products. The results of our review can highlight the gaps and align with the prevention of health risks, increasing product shelf-life, and avoiding economic losses in the tomato-based industry.