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Microalgae are widely used in the bioremediation of wastewaters due to their efficient removal of pollutants such as nitrogen, phosphorus, and contaminants of emerging concern (CECs). Siloxanes are CECs that reach wastewater treatment plants (WWTPs), leading to the production of biogas enriched with these compounds, associated with the breakdown of cogeneration equipment. The biological removal of siloxanes from wastewaters could be a sustainable alternative to the costly existing technologies, but no investigation has been performed using microalgal cultures for this purpose. This study evaluated the ability of Chlorella vulgaris to bioremediate primary (PE) and secondary (SE) urban effluents and remove volatile methylsiloxanes (VMSs). C. vulgaris grew successfully in both effluents, and approximately 86% of nitrogen and 80% of phosphorus were efficiently removed from the PE, while 52% of nitrogen and 87% of phosphorus were removed from the SE, and the presence of VMSs does not seem to have a negative influence on nutrient removal. Three out of the seven of the analysed VMSs were detected in the microalgal biomass at the end of the PE assay. However, dodecamethylcyclohexasiloxane (D6) was the one that accumulated to a greater extent, since 48% of the initial mass of D6 was detected in the biomass samples. D6 is one of the most lipophilic VMSs, which might contribute to the higher adsorption onto the surface of microalgae. Overall, the results indicate C. vulgaris’ potential to remove specific VMSs from effluents.