A study was undertaken to evaluate changes in microbial populations of nonstarter lactic acid bacteria (NSLAB), yeast and starter lactic acid bacteria (SLAB) in Gouda cheese in two independent chambers during the ripening process up to 12 weeks. No differences in populations of the tested group of microorganisms were observed at 4, 8 and 12 weeks in both the dairy and dairy-independent chambers. Populations of the analysed groups of LAB reached maximum numbers at week 4 of ripening and then gradually decreased with further aging, however with different dynamics for different species. The SLAB were the predominant microflora after salt treatment and accounted for 90% of the total microbial population in Gouda cheese. Cheese ripening led to the predomination of NSLAB and yeast populations and to a decrease in the population of SLAB. Homo- and heterofermentative vancomycin-tolerant Lactobacillus spp. constituted for the majority of the NSLAB populations. The yeast counts, at the initial populations of 4 log10 CFU/g, were increased by 2 logs after 4 weeks and were slightly reduced at 8 and 12 weeks of ripening. At 12 weeks of ripening, nonstarter Lactobacillus spp. enumerated at 25°C exceeded 90% of total LAB population while the yeast population comprised over 40% of the total LAB counts. The majority of NSLAB consisted of vancomycin-tolerant homo- and heterofermentative species of Lactobacillus.