Biogenic amines (BAs) are crucial indicators of microbial activity and pose potential safety risks in fermented foods such as cheese. This study focuses on developing and implementing a quantitative PCR (qPCR) method to detect and quantify hdcA, a non-marker gene associated with histamine bacterial biosynthesis, within the microbiota of cheese samples. The methodology includes conducting standard curves for both non-marker and marker genes before the qPCR experiments. These experiments amplify both types of genes in DNA samples from cheese microbiota, allowing for the interpolation of their abundances from the established standard curves. Abundances of the non-marker gene are then normalized against the conserved marker gene, the 16s rRNA gene, present in these samples. This approach offers a quick, easy, and reliable tool for detecting and quantifying hdcA gene in cheese. Therefore, it can be used as a convenient screening method to better understand and manage the risks linked to biogenic amines in fermented foods.