In this study, the color diversity of the PDO Munster was investigated with a special emphasis on heterogeneity and the link with biotic and abiotic factors. To do so, the evolution of the color of 33 Munster cheeses was monitored during storage. In addition, two batches of cheeses produced in the same factory were investigated for a possible link between the rind color heterogeneity and the microbiota, as well as the pH and the salt concentration. Furthermore, two cheeses exhibiting multiple undesirable brown color patches were studied in terms of microbiota composition.