Organic food products are subjected to high risk of fraud in Europe. Food traceability and authenticity of foods are mainly ensured by administrative means and there is a lack of analytical tools to authenticate organic foods. Hence, we wanted to propose a methodology that could help control and certification bodies for the authentication of organic foods. In this study we demonstrate the robustness of our original approach by comparing bacterial flora of bananas from different farming types, varieties, harvest years and geographical origins. Interestingly, the farming type could be linked to variations in bacterial diversity of bananas even if the geographical origin of bananas had the highest impact. Also, some bacterial groups have demonstrated a higher discriminative power. This opens the perspectives for the development of a food authentication tool based on the use of the natural microbial ecosystem of foods.