Dairy products harbor complex and dynamic microbial communities that contribute to their sensory properties, safety, and cultural distinctiveness. Raw milk contains a diverse microbiota shaped by seasonality, storage conditions, lactation stage, animal health, farm management, and genetics, serving as a variable starting point for further processing. Fermentation, whether spontaneous or starter driven, selects for subsets of lactic acid bacteria (LAB), yeasts, and molds, resulting in microbial succession that underpins both artisanal and industrial products such as kefir and cheese. Kefir represents a balanced LAB–yeast symbiosis, with species composition influenced by grain origin, milk type, and processing parameters, whereas the cheese microbiota reflects the interplay of starter and non-starter LAB, coagulants, ripening conditions, and “house microbiota”. Methodological factors—including DNA extraction, sequencing platform, and bioinformatic pipelines—further impact the reported microbial profiles, highlighting the need for standardization across studies. This review synthesizes current knowledge on raw milk, kefir, and cheese microbiomes, emphasizing the biological, technological, environmental, and methodological factors shaping microbial diversity. A holistic understanding of these drivers is essential to preserve product authenticity, ensure safety, and harness microbial resources for innovation in dairy biotechnology.