This dataset contains raw data on the characterization of raw materials (apple pomace, grape pomace, and molasses with sugar content estimated by Brix), semi-finished products (pomace wine) with parameters like Brix, pH, acidity, and alcohol content, as well as apple pomace fermented(composition in protein, mycotoxins, ash, various minerals), and finally apple and grape pomace vinegar: acidity, pH, alcohol content. Mass balances of different raw materials, by-products, and finished products are presented. Data were collected through trials on pilot installations and at Cogiterre's production site during the years 2021, 2022, and 2023. A comprehensive chemical analysis was performed on apple pomace vinegar to determine its composition. This analysis included the identification of polyphenols, organic acids, sugars, cations, anions, as well as alcohol and methanol content