The microalgae Chlorella sorokiniana was used for the treatment of winery wastewater (WWW). Batch experiments were initially conducted to investigate how biomass acclimatization in different media, dilution of wastewater, and addition of ammonium nitrogen (NH4-N) affect the growth of microalgae and the removal of major pollutants. Afterwards, two sequencing batch reactor (SBR) systems were tested applying different configurations and hydraulic retention times. The biomass collected at the end of the experiments was characterized for proteins, lipids, carbohydrates, amino acid profile, and the existence of lutein, β-carotene, chlorophyll a, and tocopherols. Batch experiments showed that Chlorella sorokiniana acclimatization to urban wastewater enhanced the removal of NH4-N and total phosphorus (TP). The operation of a two-stage SBR system achieved COD and NH4-N removal equal to 85 ± 9% and 91 ± 20%, respectively, while the use of a single-stage system feeding with anaerobically pretreated WWW resulted to COD and NH4-N removal of 78 ± 9% and 95 ± 9%, respectively. Analyses of biomass showed higher protein content (up to 58.8%) in batch experiments with NH4-N addition as well as in SBR experiments. The cultivation of microalgae under SBR conditions enhanced the production of pigments and tocopherols. The maximum concentrations of 1075mgkg-1, 45.5mgkg-1, and 131.2mgkg-1 were achieved for lutein, β-carotene, and tocopherols, respectively, in the one-stage system. Our findings suggested that Chlorella sorokiniana cultivation in WWW not only removed nutrients from WWW but also could potentially serve for the production of value-added ingredients used in food industry, cosmetics, and animal feedstock.