Sustainability is a leading trend in the context of food production. Additionally, consumers increasingly demand safer and less-processed products. Among the different technologies used to maintain the quality and extend the shelf-life of fresh and minimally-processed food, natural antimicrobial agents offer a promising strategy to replace conventional compounds. In this regard, phage lytic proteins or lysins, such as endolysins and virion-associated peptidoglycan hydrolases (VAPGHs), have been proposed as a viable option for the avoidance and elimination of undesirable bacteria within the food production chain. Even when applied exogenously, these proteins can degrade the bacterial cell wall maintaining their lytic activity. This feature, alongside their modular structure, which can be exploited for bioengineering, provides significant biotechnological potential. However, despite the promising properties of lysins, the main obstacle for their commercialization is the limited legal information regulating their use. This challenge underscores the need to navigate complex regulatory pathways. The primary objective of this review is to address this crucial gap and summarize the many prospective applications of endolysins during the different stages of food production. By doing so, we aim to provide clarity and insight into the regulatory challenges that must be overcome for the successful utilization of lysins.