Herein, we investigated the simultaneous photoinactivation of E. coli and degradation of an endocrine disrupting compound, 17α-ethinyl estradiol (EE2), by the ZnFe₂O₄–Ag/rGO nanocomposite. In a pure bacterial suspension, inactivation of log 7.2 was achieved in 60 min with 250 mg L⁻¹ loading of ZnFe₂O₄–Ag/rGO; however, when EE2 was present in the suspension, complete inactivation of the bacteria was achieved only after 210 min of treatment with a 500 mg L⁻¹ loading of ZnFe₂O₄–Ag/rGO. Results obtained from the bacterial membrane injury test, SEM, FTIR, and antioxidant enzyme activities indicated that resilience of E. coli decreased against the oxidative stress induced by the photocatalyst, outstripping the bacterial defense mechanism and subsequently decomposing the constituent macromolecules, ultimately causing bacterial inactivation. Scavenging experiment for different active species indicated that H₂O₂ played the most important role for bacterial inactivation and OH˙ played the most important role for EE2 degradation, showing that the roles of the active species were dissimilar for microbial inactivation and organic pollutant degradation. Bacterial inactivation was significantly affected by the presence of EE2. Thus, the antibacterial study of the photocatalysts in this system needs to be carried out with more specificity.