Food processing can lead to a reduction of contaminants, such as mycotoxins. However, for food processing operations where thermal energy is employed, it is often not clear whether a reduction of mycotoxins also results in a mitigation of the toxicological impact. This is often due to the reason that the formed degradation products are not characterized and data on their toxicity is scarce. From the perspective of an analytical chemist, the elucidation of the fate of a contaminant in a complex food matrix is extremely challenging. An overview of the analytical approaches is given here, and the application and limitations are exemplified based on cases that can be found in recent literature. As most studies rely on targeted analysis, it is not clear whether the predetermined set of compounds differs from the degradation products that are actually formed during food processing. Although untargeted analysis allows for the elucidation of the complete spectrum of degradation products, only one such study is available so far. Further pitfalls include insufficient precision, natural contamination with masked forms of mycotoxins and interferences that are caused by the food matrix. One topic that is of paramount importance for both targeted and untargeted approaches is the availability of reference standards to identity and quantity the formed degradation products. Our vision is that more studies need to be published that characterize the formed degradation products, collect data on their toxicity and thereby complete the knowledge about the mycotoxin mitigating effect during food processing.