<p>The use of microalgae in wastewater treatment offers a sustainable approach to environmental management and resource recovery. This study investigated the potential of <i>Chlorella sorokiniana</i> cultivated in different types of agro-industrial wastewater, including effluents from dairy processing, citrus fresh juice production, and chili sauce manufacturing, for simultaneous pollutants removal and high-value biomass generation. The microalgae were cultivated under continuous and periodic illumination (51.51 and 17.62&#xa0;μmol photons m⁻²&#xa0;s⁻¹, respectively) in 2-L or 5-L sequencing batch reactors, with and without nitrogen supplementation, using both one-stage and two-stage bioreactor systems. Biomass growth rates were comparable under both continuous (0.13 ± 0.9&#xa0;mg&#xa0;day⁻¹) and periodic illumination (0.12 ± 0.12&#xa0;mg&#xa0;day⁻¹), with no statistically significant differences observed among the various types of wastewater. The removal of COD and NH₄-N in one-stage experiments ranged up to 90 ± 3% and 89 ± 3%, respectively, while COD removal was higher in experiments conducted under periodical illumination and with no nitrogen addition. No significant differences in the protein content of biomass were observed among the tested wastewater types, while nitrogen supplementation enhanced protein biosynthesis. In one-stage experiments, the highest lutein and chlorophyll-<i>a</i> concentrations were observed in the bioreactor with chili sauce wastewater, reaching 12.21&#xa0;mg&#xa0;g⁻¹ and 62.5&#xa0;mg&#xa0;g⁻¹, respectively, while periodic illumination improved the ability of microalgae to synthesize β-carotene and chlorophyll-a. In two stage experiments, the higher concentrations of lutein were observed after the end of the 1st stage. Based on the results, <i>C. sorokiniana</i> can successfully grow in various types of agro-industrial wastewater, efficiently remove pollutants, and yield biomass enriched with valuable nutrients, including pigments and proteins.</p>