Incomplete removal of contaminants of emerging concern (CECs) has been reported for conventional wastewater treatment technologies. Microalgae-based treatment has recently gained interest thanks to simultaneous removal capacity of organic and inorganic compounds and potentially CECs. In this study, a lab-scale monoculture of Chlorella vulgaris and mixed microalgal-bacterial culture were compared in terms of removal of 28 CECs (bisphenols, 2018 EU Watch List substances, including neonicotinoids, pharmaceuticals, selected transformation products). The removal pathways in light and dark abiotic controls were also studied. Batch photobioreactors were run at hydraulic retention times of 11–12 days and CECs spiked at environmentally relevant concentrations (1–20 μg L⁻¹). The mixed culture was better at removing bisphenols, compared to C. vulgaris. Bisphenols’ log K_ow was significant in removal pathways, where bisphenols with high log K_ow were removed abiotically while bisphenols with low log K_ow were mainly biodegraded. The removal degrees and the pathways of pharmaceuticals and EU Watch List substances were comparable between both cultures, showing no impact of log K_ow for most compounds; however, the removal with C. vulgaris was faster for some. High log K_ow was associated with high removal of estradiol in abiotic controls, showing the importance of adsorption onto biomass and suspended matter.