Cheese production is a useful model to study food ecosystem dynamics as these fermented products illustrate opposing roles of adventitious microbes involved—as spoilage agents and as beneficial members of the microbial consortium—both of which influence final product quality. Recently, application of rRNA marker gene surveys to define the modes of microbial transmission across space and time in cheese production has provided unique insight into these important commercial fermentations. Cheese fermentations are well known to be initiated by starter cultures, however recent studies suggest that adventitious microbiota is influenced by environmental factors thus potentially contributing to the “regional character” often attributed to specific products. Moreover, advances in sensor technology now allows simultaneous monitoring of food production facilities for various environmental parameters including: temperature, relative humidity, volatile organic carbon, CO₂, dust accumulation and human traffic. Integration of sensor data with microbiota surveys provides unique insight into mechanisms of microbial dispersal and persistence throughout seasonal or process-related environmental changes. Elucidating microbial ecosystems and spatial characteristics present in cheese production environments identifies the fundamental drivers of microbial biogeography with practical implications for all food production systems.