Bacteriophages are among the most important factors affecting the performance of lactic acid bacteria in the dairy industry and play a critical role in the success or failure of fermentation processes. The widespread presence of lactococcal and streptococcal phages in raw milk, whey, production environments, processing equipment, and prophages harbored within lysogenic starter cultures increases the risk of phage contamination throughout cheese manufacturing. Phage infection can reduce starter culture activity, delay acidification, disrupt fermentation, and alter the physicochemical characteristics of cheese, ultimately affecting product quality and manufacturing efficiency. These changes may lead to economic losses and create favorable conditions for the growth of spoilage microorganisms and foodborne pathogens, thereby raising concerns related to food safety and biosafety. In addition, certain bacteriophages may contribute to horizontal gene transfer and influence the dynamics of microbial populations within dairy ecosystems. This review examines the major sources of phage contamination in cheese production, the mechanisms through which bacteriophages affect fermentation performance and cheese quality, and the biosafety implications associated with their presence in dairy systems. Furthermore, current strategies for phage monitoring, prevention, and control are discussed, including the use of phage-resistant starter cultures, phage surveillance programs, and other risk mitigation approaches aimed at improving process stability and enhancing biosafety in the dairy industry.