Biogenic amines (BAs) are considered a potential microbiological toxicological hazard in aged cheese. Risk mitigation strategies include good hygiene practice measures, thermal treatment of milk and the use of competitive dairy cultures. The aim of this study was to evaluate the amount of BAs—tryptamine, β-phenylethylamine, putrescine, cadaverine, histamine, tyramine, spermidine and spermine—in the core and rind of cheeses ripened by bacteria (n = 61) and by mold cultures (n = 8). The microbial communities were counted, and the dominant lactic acid bacteria (LAB) were identified, corresponding to the BA concentrations. The total BA content was highest in the core of semi-hard cheeses (353.98 mg/kg), followed by mold cheeses (248.99 mg/kg) and lowest in hard cheeses (157.38 mg/kg). The highest amount of BAs was present in the rind of cheeses with mold (240.52 mg/kg), followed by semi-hard (174.99 mg/kg) and hard cheeses (107.21 mg/kg). Tyramine was the most abundant BA, represented by 75.4% in mold cheeses, 41.3% in hard cheese and 35% of total BAs in semi-hard cheeses. Histamine was present above the defined European maximum level (ML) of 100 mg/kg in only two semi-hard and three hard cheeses. High amount of BAs (above 600 mg/kg) in cheeses, mainly tyramine, were associated with the presence of Enterococcus durans, while negligible BA concentrations were found in cheeses ripened with Lacticaseibacillus rhamnosus, Lactococcus lactis or Lacticaseibacillus paracasei cultures. This study has shown that retailed cheese varieties produced with commercial bacterial or mold cultures have acceptable levels of biogenic amines with respect to consumers.