The antimicrobial photodynamic activity (aPDA) in fungal and bacterial strains of supramolecular adducts formed between the anionic photosensitizer (PS) Rose Bengal (RB2-) and aromatic polycations derived from (p-vinylbenzyl)triethylammonium chloride was evaluated. Stable supramolecular adducts with dissociation constants Kd ≈ 5 μM showed photosensitizing properties suitable for generating singlet oxygen (ΦΔ = 0.5 ± 0.1) with the added advantage of improving the photostability of the xanthenic dye. However, the aPDA of both free and supramolecular RB2- was highly dependent on the type of microorganism treated, indicating the importance of specific interactions between the different cell wall structures of the microbe and the PSs. Indeed, in the case of Gram-positive Staphylococcus aureus, the aPDA of molecular and supramolecular PSs was highly effective. Instead, in the case of Gram-negative Escherichia coli, only the RB2-:polycation adducts showed aPDA, while RB2- alone was inefficient, but in the case of Candida tropicalis, the opposite behavior was observed. Therefore, the present results indicate the potential of supramolecular chemistry to obtain aPDA à la carte depending on the target microbe and the PS properties.