In this study, the evolution of microbial counts, biogenic amine contents, and related parameters (pH, moisture, and proteolysis) in goat cheese made from fresh raw milk or raw milk stored for 48 h at 4°C was examined. In both cases the milk was nonpasteurized. This study was designed to evaluate the effect of milk quality on the profile of biogenic amines in relation to the evolution of the microbial population during cheese making. Cheese made from raw milk stored for 48 h at 4°C showed the highest microbial counts and biogenic amine levels. The storage of milk under refrigeration caused significant increases in the levels of some microbial and biogenic amines during ripening, but not initially. Tyramine was the main biogenic amine in the two cheeses tested, followed by cadaverine. However, the main differences in amine contents between batches were found for putrescine, histamine, and β-phenylethylamine, whose levels were more than twofold higher in samples from raw milk refrigerated for 48 h than in samples from fresh milk.