The effect of Zataria multiflora Boiss. (Z.multiflora) essential oils (EO) on biogenic amines (BAs) production and microbial counts in Gouda cheese has been investigated. Zataria multiflora was added to milk in different concentrations (0·05, 0·1, 0·2 and 0·4% (v/v)). The BAs (tyramine and histamine) were measured by RP-HPLC, following extraction from the cheese. Various microbiological analyses (aerobic mesophilic bacteria, enterococci, mesophilic lactobacilli, Enterobacteriaceae, lactococci and yeasts) were performed during ripening using the viable plate count method on specific culture media. The overall acceptability of cheeses was investigated by seven panellists. All the samples containing different concentrations of EO were acceptable to the panellists. Also, Gouda cheeses with 0·2% Z.multiflora EO showed the highest acceptability among all the samples. At the end of maturation period, 0·1, 0·2 and 0·4% Z.multiflora EO reduced tyramine and histamine significantly to 5%, 22% and 44% for tyramine and 14%, 29% and 46% for histamine, respectively, when compared to the control group. The increase of Z.multiflora EO concentrations led to further decrease in BAs content and microbial counts. The maximum microbiological reduction was observed in yeasts, and minimum microbiological reduction was seen in Enterobacteriaceae counts. Zataria multiflora EO could be used for reduction of BAs and also as a flavouring agent in Gouda cheese and could contribute to consumers' health. The presence of biogenic amines in cheese has a serious impact on public health. Besides, there is growing concern about the use of chemical preservatives and the food industry is looking for new natural preservation methods. Zataria multiflora Boiss. essential oil is well known for its antimicrobial effects, and we attempted to reduce biogenic amines formation in Gouda cheese using Z.multiflora Boiss. essential oil as a natural additive. Furthermore, the desirable organoleptic qualities such as flavour, odour, texture and colour were achieved by adding Z.multiflora Boiss. to cheese.