Cooking is an important processing method, that has been used since ancient times in order to both ensure microbiological safety and give desired organoleptic properties to the cooked food. Fish and other seafood products are highly sensitive to thermal treatments and the application of severe heat can result in negative consequences on sensory and nutritional parameters, as well as other quality attributes of the thermally processed products. To avoid such undesired effects and to extend the shelf life of these perishable products, both the heat processing methods and the assessment techniques used to monitor the process should be optimized. In this review paper, the most common cooking methods and some innovative ones will first be presented with a brief discussion of their impact on seafood quality. The main methods used for monitoring heat treatments will then be reviewed with a special focus on spectroscopic techniques, which are known to be rapid and non-destructive methods compared to traditional approaches. Finally, viewpoints of the current challenges will be discussed and possible directions for future applications and research will be suggested. The literature presented in this review clearly demonstrates the potential of spectroscopic techniques, coupled with chemometric tools, for online monitoring of heat-induced changes resulting from the application of thermal treatments of seafood. The use of fluorescence hyperspectral imaging is especially promising, as the technique combines the merits of both fluorescence spectroscopy (high sensitivity and selectivity) and hyperspectral imaging (spatial dimension). With further research and investigation, the few current limitations of monitoring thermal treatments by spectroscopy can be addressed, thus enabling the use of spectroscopic techniques as a routine tool in the seafood industry.