Olive mill wastewater (OMWW) has a significant potency as a source of value-added phytochemicals, including phenolic antioxidants, of which hydroxytyrosol (HTyr) is a molecule of high interest to the nutraceutical industry, owing to several associated health benefits. With the aim of seeking a productive recovery of antioxidants, mainly HTyr, this research utilized lagoon and decanter OMWWs. Separation of phenolic antioxidants from both wastewaters, which were concentrated with a mechanical vapor recompression evaporator, was achieved by applying a multistage recovery process, consisting of complementary steps in the order of acidification, delipidization, solvent extraction, and solid-phase extraction. While initial concentrations of HTyr in acidified lagoon and decanter concentrates were 0.4 mg/g and 2.9 mg/g, respectively, their recoveries reached maximum values of 6.6 and 4.7 mg/g, with an ethanol/(NH₄)₂SO₄-based aqueous two-phase system (ATPS) by eliminating considerable amounts of carbohydrates (59–90%) and proteins (90–92%). Further purification of the extracts of the ATPS was achieved by using XAD16N resin with high HTyr selectivity. The application of supplementary stages is critical for successful recovery to increase the amount of free phenolic antioxidants and to enhance the purity of the crude extracts. At the end of the multistage recovery process, 80% HTyr and 61% total phenols were successfully recovered by removing 88–97% carbohydrates and 97–100% proteins from lagoon and decanter concentrates. The results revealed that ethanol/salt-based ATPS is a suitable alternative, allowing the use of a safer solvent and providing a higher HTyr recovery from OMWW compared with that of conventional extraction with ethyl acetate which provided only 3.2 mg/g HTyr recovery from both of the samples.