Background/Objectives: The composition and function of gut microbiome is significantly influenced by dietary factors. Growing evidence suggests that A1-type and A2-type beta casein (β-CN) may exert distinct effects on the gut environment, with implications for digestive discomfort and broader health outcomes. This review summarizes current evidence on how milk-derived A1 and A2 β-CN affect the gut microbiota. Methods: We conducted a literature search using PubMed, Web of Science, and Scopus to identify studies examining effects of milk β-CN on gut microbiota. Results: A total of eight studies were included. Results show inconsistencies within the limited number of studies. However, compared to A2, A1 β-CN was more frequently associated with dysbiosis and an increased abundance of potentially pathogenic species. Conversely, A2 β-CN promoted microbial diversity, which is linked to improved gut integrity and metabolic health. Conclusions: These findings suggest that β-CN variants distinctly influence the gut microbiota composition, and results were more significant in immunosuppressed subjects or those with other underlying health conditions, indicating that dairy products rich in A2 β-CN may offer advantages in personalized dietary management. However, well-designed human studies are essential to translate findings from rodent models to clinically relevant outcomes and future research should focus on mechanistic exploration and population-specific responses.