The present work aims to compare two acetification profiles coming from the same starter culture but using different raw materials. For this purpose, the composition and natural behavior of the microbiota present throughout both processes were compared employing a metaproteomic analysis and, especially, focusing on the protein profile of K. europaeus from anexhaustive quantitative approach. A comparison of vinegar profiles using two natural raw materials (fine wine and craft beer) under a strategy that employs a submerged culture and a semi-continuous operating mode could improve the current knowledge about the influence of the raw materials on the organoleptic properties and quality of industrially elaborated vinegars.