In this work, the ability of amphiphilic phthalocyanine (Pc) photosensitizers (PS) (Zn(II)Pcs PS1, PS2 and PS3) to assemble into cationic nanoparticles in water and to photo‐inactivate bacterial strains is demonstrated. All the synthesized Zn(II)Pcs exhibit an AABB functionalization pattern, having a binaphthyloxy‐linked bisisoindole (AA) functionalized at the chiral binaphthol core with branched (PS1) or linear (PS2 and PS3) poly‐ammonium chains, and two non‐functionalized isoindole rings (BB). The aggregation behavior and the stability of the nanoparticles formed by the three PS in water is studied by UV‐vis, fluorescence and circular dichroism (CD) spectroscopies, and their shape and size is determined by transmission electron microscopy (TEM) and dynamic light scattering (DLS). The PS nanoparticles proved efficient in the photoinactivation of S. aureus and E. coli. Although PS2 and PS3 present better photophysical features in their monomeric form (i.e., improved singlet oxygen quantum yield), PS1 is more effective in killing both types of strains, especially the gram‐negative E. coli. This observation may derive from the low stability found for PS1 nanoparticles, which easily disassemble after binding to the bacteria surface, recovering the photophysical properties of the non‐aggregated species.This article is protected by copyright. All rights reserved