Physico-chemical interactions between nanoparticles and cell membranes play a crucial role in determining the cytotoxicity of nanoparticles, which may thereby vary depending on the nature of the target microorganisms. We investigated the responses of two different models of unicellular bacteria to cerium oxide (CeO2) nanoparticles. These organisms are: Synechocystis PCC6803 a representative of environmentally important cyanobacterial organisms (producer of biomass for aquatic food chains), and Escherichia coli a representative of intestine-colonizing bacteria. Coupling physico-chemical (adsorption isotherms and electrophoretic mobility), biological (survival tests), microscopical (SEM, TEM and EDS) and spectroscopic (XANES) methods, we enlightened two distinct mechanisms for the CeO2 nanoparticles toxicological impact: A ‘direct’ mechanism that requires a close contact between nanoparticles and cell membranes, and an ‘indirect’ influence elicited by the acidity of nanoparticles stabilizing agents. We showed that E. coli is sensitive to the ‘direct’ effects of nanoparticles, whereas Synechocystis being protected by extracellular polymeric substances preventing direct cellular contacts is sensitive only to the ‘indirect’ mechanism. Consequently, our findings demonstrate the importance of the ‘direct/indirect’ effects of nanoparticles on cell fitness, a phenomenon that should be systematically investigated with appropriate techniques and dose metrics to make meaningful environmental and/or health recommendations.