Antioxidants play a significant role in human health, protecting against a variety of diseases. Therefore, the development of products with antioxidant activity is becoming increasingly prominent in the human lifestyle. New antioxidant drinks containing different percentages of pomegranate, blackberries, red grapes, and aronia have been designed, developed, and manufactured by a local industry. The comprehensive characterization of the drinks’ constituents has been deemed necessary to evaluate their bioactivity. Thus, LC-qTOFMS has been selected, due to its sensitivity and structure identification capability. Both data-dependent and -independent acquisition modes have been utilized. The data have been treated according to a novel, newly designed workflow based on MS-DIAL and MZmine for suspect, as well as target screening. The classical MS-DIAL workflow has been modified to perform suspect and target screening in an automatic way. Furthermore, a novel methodology based on a compiled bioactivity-driven suspect list was developed and expanded with combinatorial enumeration to include metabolism products of the highlighted metabolites. Compounds belonging to ontologies with possible antioxidant capacity have been identified, such as flavonoids, amino acids, and fatty acids, which could be beneficial to human health, revealing the importance of the produced drinks as well as the efficacy of the new in-house developed workflow.