The microbiota of ripening cheese is dominated by lactic acid bacteria, which are either added as starters and adjunct cultures, or originate from the production and processing environments (non starter or NSLAB). After curd formation and pressing, starters have reached high numbers, but their viability then decreases due to lactose depletion, salt addition, low pH and temperature. Starter autolysis releases cellular contents, including nutrients and enzymes, into the cheese matrix. During ripening, NSLAB may attain cell densities up to 8 logs of colony-forming units after 3–9 mo. Depending on the species and strains, their metabolic activity may contribute to defects or inconsistency in cheese quality as well as to the development of typical cheese flavor. Studies using qPCR and RT-qPCR have shown that the starters survive and dominate the cheese microbiota over 6 mo. The lowering costs of high throughput sequencing have contributed to understanding the changing composition of the cheese microbial community. The availability of gene and genome sequences has enabled targeted detection of specific cheese microbes and their gene expression over the ripening period. The application of RT-qPCR has revealed how the expression of genes encoding peptide transporters and peptidases of Lactobacillus paracasei is stimulated in mixed culture compared with pure culture in cheese slurry. Integrated systems biology is needed to combine the multiple perspectives of post-genomics technologies to elucidate the metabolic interactions among microorganisms. Future research should delve into the variation in cell physiology within the microbial populations, as spatial distribution within the cheese matrix will lead to microenvironments that could impact localized interactions of starters and NSLAB. Microbial community modeling can contribute to improving the efficiency and reduce the cost of food processes such as cheese ripening.