Gouda cheese is one of the most produced cheese types worldwide. Despite its industrialized production, a typical Gouda cheese starter culture is undefined. It is composed of an unknown mixture of different strains of Lactococcus and Leuconostoc species, which have different functions during cheese production and ripening. During ripening, typical nonstarter lactic acid bacteria (NSLAB), such as Lacticaseibacillus paracasei and Lactiplantibacillus plantarum, arise. Sometimes, unusual bacteria may be present, which all may produce biogenic amines or result in other defects, such as cracks and spots. Also, Listeria monocytogenes contamination is still of concern. This paper highlights new insights into the microbiota and current defects of Gouda cheese production.