The occurrence of foodborne diseases and food poisoning due to the consumption of contaminated foods is increasing nowadays, thus become a major threat to food industries in particular. In order to overcome this problem, prevention must be taken at the early stages of food preparation like sanitization. Typically, chemically based antimicrobial sanitisers were used in food industries to remove dirt and microbial population on food surfaces or food equipment. However, the emergence of microbial resistance and consumer awareness on the formation of carcinogenic compounds and safety issues in long term effects has led researchers to find an alternative. Therefore, a study was conducted to find a natural food sanitiser that was able to minimize the number of harmful bacteria without a change in the food quality and safety. In this study, the stability of Cosmos caudatus extract at different pH (pH 3, pH 7, pH 8 and pH 11) and temperatures (25°C, 30°C, 50°C, 80°C and 121°C) were determined for suitability as food sanitiser. The identification and quantification of this plant extract also were performed using HPLC and LC-MS/MS analysis to detect the major compounds which contributed to the biological activity of C. caudatus extract. Generally, results showed that the antimicrobial activity of C. caudatus extract was stable after exposure to various pH and temperatures, in fact, the extract increased its antimicrobial activity at lower acidity (pH 3) and higher temperature (50°C) against most pathogens. Furthermore, quercetin 3-O-rhamnoside was identified as a major compound in C. caudatus extract with the relative amounts of 29.66 mg/g. It can be concluded that C. caudatus extract is stable when exposed to various pH and temperatures. These useful findings have proved the antimicrobial stability of C. caudatus extract after exposure to several pH and temperatures thus can be further developed as a food sanitiser in food industries.