This study reports the first attempt of a citrate-modified photo-Fenton (PF) application at near-neutral pH (7.5–8.5, tap water) to disinfect Escherichia coli (as model bacterium), in Chlorella vulgaris cultures. The conditions are aimed towards bacterial inactivation, while minimizing the detrimental effect on microalgae viability. The presence of microalgae accelerates H2O2 consumption and may affect bacterial disinfection due to faster H2O2 depletion. Supplementation of citric acid before PF improved the inactivation efficacy by 1.34–1.96 logU, alongside with a notably lower microalgae inactivation. Citric acid also considerably increased the lifetime of dissolved iron and prevented aggregation of microalgae, which was caused by Fe2+ addition. While these aggregates do not impact the already short lifetime of dissolved iron, they impede the citrate-favored homogeneous process that mainly inactivates E. coli. Finally, an integrated mechanism for C. vulgaris inactivation is suggested and compared with the one of E. coli.