Abstract Biotransformation and biodegradation of estrogenic compounds by bacteria and even fungi have been reported widely, but the role of microalgae in the elimination of estrogens from municipal wastewater treatment plants and their interaction with other microorganisms in wastewater are not clear. This study reported the feasibility of repeatedly removing a mixture of 17β-estradiol (E2) and 17α-ethinylestradiol (EE2), each was 100 μg L−1, from primary settled municipal sewage by Selenastrum capricornutum (SC), a ubiquitous microalga, in four exposure cycles, each lasted 7 days, and how they interacted with the microbial consortium in sewage. Mixed estrogen in sewage stimulated the growth of SC, and the indigenous microorganisms in sewage also affected the microalgal growth. The indigenous microorganisms, particularly bacteria, could easily remove E2 (with 99.5% removal), so the role of SC was insignificant. On the contrary, EE2 was difficult to remove by indigenous microorganisms but the removal was significantly enhanced by SC, with almost all spiked EE2 being removed, even at the end of the fourth cycle (with 99.0% removal). These results indicated that SC, together with the indigenous microorganisms in wastewater, could be repeatedly used for simultaneous removal of E2 and EE2 from municipal sewage.