The remarkable global diversity in long-ripened cheese production can be attributed to the adaptability of the cheese microbiota. Most cheese types involve intricate microbial ecosystems, primarily represented by lactic acid bacteria (LAB). The present study aims to review the microbial community’s diversity in dairy fermentation processes, focusing on two famous Italian cheeses, Grana Padano and Parmigiano Reggiano, produced using natural whey starter (NWS). NWS, created by retaining whey from the previous day’s cheese batches, forms a microbiological connection between daily cheese productions. Through this technique, a dynamic microbiota colonizes the curd and influences cheese ripening. The back-slopping method in NWS preparation ensures the survival of diverse biotypes, providing a complex microbial community in which interactions among microorganisms are critical to ensuring its technological functionality. As highlighted in this review, the presence of microbial cells alone does not guarantee technological relevance. Critical microorganisms can grow and colonize the curd and cheese. This complexity enables NWS to adapt to artisanal production technologies while considering variations in raw milk microbiota, inhibitory compounds, and manufacturing conditions. This critical review aims to discuss NWS as a key factor in cheese making, considering microbial communities’ ability to evolve under different selective pressures and biotic and abiotic stresses.