AbstractStructure–activity relationships have been widely reported for porphyrin and phthalocyanine photosensitizers, but not for phenothiazinium derivatives. Here, four phenothiazinium salts (methylene blue, toluidine blue O, 1,9‐dimethyl methylene blue and the pentacyclic derivative DO15) were used to investigate how the ability to damage membranes is affected by membrane/solution partition, photophysical properties and tendency to aggregation of the photosensitizer. These two latter aspects were studied both in isotropic solutions and in membranes. Membrane damage was assessed by leakage of a fluorescent probe entrapped in liposomes and by generation of thiobarbituric acid‐reactive species (TBARS), while structural changes at the lipid bilayer were detected by small‐angle X‐ray scattering. We observed that all compounds had similar singlet‐oxygen quantum yields in ethanol, but only the photosensitizers that had higher membrane/solution partition (1,9‐dimethyl methylene blue and DO15, the latter having the higher value) could permeabilize the lipid bilayer. Moreover, of these two photosensitizers, only DO15 altered membrane structure, a result that was attributed to its destabilization of higher order aggregates, generation of higher amounts of singlet oxygen within the membranes and effective electron‐transfer reaction within its dimers. We concluded that membrane‐based protocols can provide a better insight on the photodynamic efficiency of the photosensitizer.