Due to the potential health risks of synthetic food preservatives, there has been a noticeable increase in interest in finding natural food preservatives during the past few decades. The goal of this study was to investigate the use of a natural extract of Myrrh resin as an antimicrobial agent. The antioxidant properties of Myrrh resin extract (MRE) were analyzed using HPLC and GC–MS. The results showed that MRE contained potent antioxidant compounds, including 19 compounds, with the dominant compound being kaempferol, which had the highest value of 1896 µg/g. Quercetin was found to be the second most abundant compound, with a value of 520 µg/g.The efficacy of MRE as an antimicrobial agent against both Gram-positive and Gram-negative bacteria was tested, and its application in Cacao beverages was also studied. The results demonstrated that MRE was highly effective against all the tested bacteria both in vitro and in the total bacterial count of the produced cacao beverage. Additionally, the fungi in the cacao beverage were completely inhibited at all tested concentrations of MRE. The total soluble solids (TSS), pH value, and acidity of the produced untreated, treated cacao beverage with MRE and sodium benzoate were carried out, and all values mentioned were almost the same, with no differences noted. The sensory evaluation of Cacao beverage showed that the MRE had a minor impact on taste, odor, color, and texture of the produced cacao beverage in comparison with the control sample, which was very acceptable for judgments and recorded 95, 88, and 94 for the control and treated samples, respectively. Furthermore, the anti-cancer properties of MRE were evaluated, revealing significant cytotoxic effects against colon cancer (HCT) and liver cancer (HEPG2) cell lines. The IC50 values for HCT and HEPG2 cells were 55.69 µg/ml and 70.78 µg/ml, respectively, indicating the potential of MRE as an anti-cancer agent.