Electronic Noses (ENs) are attracting a relevant interest as valuable monitoring tool in several fields, between which the food industry, with special emphasis on microbial contamination detection on food products. Herein we present the ability of an Electronic Nose to early identify the fungi contamination in green coffee. The detection of mold in green coffee was achieved thanks to the cooperative use of different chemical and microbiological (fenotipic) techniques aimed to detect the secondary metabolites. Obtained results strongly recommend the use of the ENs as screening tools in industrial quality control laboratories, emphasizing at the same time some limits still affecting the sensor technology.