The mounting demand for biomolecules in industry, particularly in regard to antioxidant-rich food supplements and monoclonal antibodies, has been compelling pharmaceutical companies to invest in this field and to redesign the production of active pharmaceutical ingredients (APIs) by implementing the principles of green chemistry and circular economy. For example, by promoting the use of renewable feedstocks, such as biowaste from the food sector, it is possible to simultaneously avoid the footprint of chemical synthesis and reduce the price of raw materials. Aqueous two-phase systems (ATPS), or aqueous biphasic systems (ABS), have been gaining relevance in the extraction of biomolecules such as proteins, vitamins, and lipids, given their low price, low energy demand, large scale-up potential, and considerable biocompatibility. These features make ATPS very powerful primary concentration steps in industrial processes, which become especially eco-friendly when combined with green solvents such as ethyl lactate and salts of organic basis. Among some common biomolecules in biowaste, cyanocobalamin (Cya), epicatechin (Epi), folic acid (Fol), and syringic acid (Syr) possess very interesting properties given their relatively large presence and strong antioxidant potential. Therefore, in this work, these four well-known biomolecules were extracted in the ATPS {ethyl lactate (1) + sodium potassium tartrate (2) + water (3)} at 298.15 K and 0.1 MPa. This eco-friendly ATPS allowed low mass losses (< 3 %) in the liquid−liquid extractions, having attained the maximum partition coefficients (K = 6.5 ± 0.4) and extraction efficiencies (E = 90.7 ± 0.2 %) for cyanocobalamin using the longest tie-line (TLL = 70.73 m%). Conversely, for the same tie-line composition, the smallest performance indicators (K = 1.25 ± 0.03 and E = 69.3 ± 0.2 %) were obtained for folic acid. The partition studies were performed after careful evaluation of the effect of pH on the mean electrical charge of each biomolecule.