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Microalgae are capable of assimilating nutrients from wastewater (WW), producing clean water and biomass rich in bioactive compounds that need to be recovered from inside the microalgal cell. This work investigated subcritical water (SW) extraction to collect high-value compounds from the microalga Tetradesmus obliquus after treating poultry WW. The treatment efficiency was evaluated in terms of total Kjeldahl nitrogen (TKN), phosphate, chemical oxygen demand (COD) and metals. T. obliquus was able to remove 77% TKN, 50% phosphate, 84% COD, and metals (48–89%) within legislation values. SW extraction was performed at 170 °C and 30 bar for 10 min. SW allowed the extraction of total phenols (1.073 mg GAE/mL extract) and total flavonoids (0.111 mg CAT/mL extract) with high antioxidant activity (IC50 value, 7.18 µg/mL). The microalga was shown to be a source of organic compounds of commercial value (e.g., squalene). Finally, the SW conditions allowed the removal of pathogens and metals in the extracts and residues to values in accordance with legislation, assuring their safety for feed or agriculture applications. [ABSTRACT FROM AUTHOR]