Azole fungicides have been reported to be the most effective active substances in the control of Fusarium Head Blight (FHB) and in the reduction of the main mycotoxins that occur in cereal grain, such as deoxynivalenol (DON). Four field experiments have been conducted in North West Italy, over a period of 2 growing seasons, in order to evaluate the effect of azole fungicide (prothioconazole) applications on the prevalence of emerging mycotoxins in common winter wheat under naturally-infected field conditions. Wheat samples have been analysed by means of a diluteand-shoot multi-mycotoxin LC-MS/MS method. Twenty fungal metabolites were detected: enniatins, aurofusarin, moniliformin, equisetin, DON, deoxynivalenol-3-glucoside, culmorin, bikaverin, beauvericin, fumonisins, fusaric acid, 3-acetyldeoxynivalenol, 15-acetyldeoxynivalenol, nivalenol, zearalenone, decalonectrin, butenolide, tentoxin, alternariol and alternariol methyl ether. The most abundant fungal metabolites were DON and culmorin, with an average contamination in the untreated control of 1,360 µg/kg and 875 µg/kg, respectively, in the growing season with the highest disease pressure (2011)(2012). On average, the results have shown that the fungicide application significantly reduced the enniatins (from 127 µg/kg to 46 µg/kg), aurofusarin (from 62 µg/kg to 21 µg/kg), moniliformin (from 32 µg/kg to 16 µg/kg), tentoxin (from 5.2 µg/kg to 2.5 µg/kg) and equisetin (from 0.72 µg/kg to 0.06 µg/kg) contents in all the experiments. However, DON, deoxynivalenol-3-glucoside and culmorin were only significantly reduced in the growing season with the highest disease pressure. The other fungal metabolites were mainly found in traces in the untreated plots. These results, which have been obtained in different environmental and agronomic conditions, have underlined for the first time that the fungicide usually applied to control the FHB and DON content, also consistently reduces the main emerging mycotoxins of winter wheat in temperate areas.