Herein, the photodynamic activity of phthalocyanine (pc)‐assembled nanoparticles against bacterial strains is demonstrated. The photosensitizers (PS) studied in this work are two chiral ZnIIPcs (PS‐1 and PS‐2), with an AABB geometry (where A and B refer to differently substituted isoindole constituents). They contain differently functionalized, chiral binaphthyloxy‐linked A isoindole units, which determine the hydrophobicity of the system, and cationic methyl pyridinium moieties in the other two isoindoles to embody hydrophilicity. Both compounds have the ability to self‐assemble into nanoparticles in aqueous media and have proved efficient in the photo‐inactivation of Staphylococcus aureus and Escherichia coli, selected as models of Gram‐positive and Gram‐negative bacteria. The average size of the nanoparticles was determined by substitution at the binaphthyl core and, in turn, influences the toxicity of the PS. Thus, PS‐1, presenting a nonsubstituted binaphthyl core, forms larger nanoparticles with a larger cationic surface than the octyl‐functionalized PS‐2. Although both PSs present similar structure and photophysical features, the self‐assembled nanostructures of PS‐1 are more effective at killing both types of strain, showing an outstanding photo‐inactivation capacity with the Gram‐negative E. coli.