Cheeses made with unpasteurized milk are a safety concern due to possible contamination with foodborne pathogens. Listeria monocytogenes and Escherichia coli O157:H7 have been implicated in several outbreaks and recalls linked to Gouda cheese made with unpasteurized milk. The U.S. Food and Drug Administration Code of Federal Regulations requires cheeses made with unpasteurized milk to be aged at a minimum of 1.7°C for at least 60 days before entering interstate commerce. The goal of this study was (i) to assess the population dynamics of L. monocytogenes and E. coli O157:H7 during aging of Gouda cheese when the pathogens were inoculated into the unpasteurized milk used for manufacture and (ii) to compare the native microbial populations throughout manufacture and aging. Unpasteurized milk was inoculated with L. monocytogenes at 1 or 3 log CFU/mL or with E. coli O157:H7 at 1 log CFU/mL, and Gouda cheese was manufactured in laboratory-scale or pilot plant-scale settings. Cheeses were stored at 10°C for at least 90 days, and some cheeses were stored up to 163 days. Initial native microflora populations in unpasteurized milk did not differ significantly for laboratory-scale or pilot plant-scale trials, and population dynamics trended similarly throughout cheese manufacture and aging. During manufacture, approximately 81% of the total L. monocytogenes and E. coli O157:H7 populations was found in the curd samples. At an inoculation level of 1 log CFU/mL, L. monocytogenes survived in the cheese beyond 60 days in four of five trials. In contrast, E. coli O157:H7 was detected beyond 60 days in only one trial. At the higher 3-log inoculation level, the population of L. monocytogenes increased significantly from 3.96 ± 0.07 log CFU/g at the beginning of aging to 6.00 ± 0.73 log CFU/g after 150 days, corresponding to a growth rate of 0.04 ± 0.02 log CFU/g/day. The types of native microflora assessed included Enterobacteriaceae, lactic acid bacteria, mesophilic bacteria, and yeasts and molds. Generally, lactic acid and mesophilic bacterial populations remained consistent at approximately 8 to 9 log CFU/g during aging, whereas yeast and mold populations steadily increased. The data from this study will contribute to knowledge about survival of these pathogens during Gouda cheese production and will help researchers assess the risks of illness from consumption of Gouda cheese made with unpasteurized milk.