Processing citrus fruits results in significant amount of wastes; however, citrus by-products still contain high amounts of polyphenolic and other bioactive value-added compounds. In addition, bergamot (Citrus bergamia) wastes contain two compounds—brutieridin and melitidin—which exhibit statin-like properties. Recently, novel fermented products containing bioactive compounds received increasing attention because of their health-promoting functions. In this study, the bioconversion of citrus wastes in vinegars with high content in bioactive and aromatic compounds was performed, detecting a high permanence at the end of the process of the main compounds of interest, especially brutieridin and melitidin. In addition, the sensory analysis of the vinegars was performed, obtaining good performances. According to the adopted preselection procedure, 50 out of the 54 strains of acetic acid bacteria were excluded because of their low aptitude to grow in the tested conditions. The best vinegar was produced from citrus wine at pH 2.90 using the Acetobacter aceti strain DSM_3508T as microbial starter. This research has demonstrated—for the first time—the possibility to produce citrus vinegar at high content of brutieridin and melitidin and other bioactive compounds using selected microbial starters.