Antimicrobial photodynamic therapy (aPDT) is a promising strategy to overcome issues related to antibiotic resistance. Here we describe the rationale for designing new photosensitizers based on the functionalization of bodipy dyes with triarylphosphonium rotaxanes and provide an in-depth characterization of their photophysical properties, applying different spectroscopic techniques, including ultrafast transient absorption spectroscopy. While the addition of halogen atoms to some of our structures provides them the ability to efficiently produce singlet oxygen in organic solvents, such property is suppressed in water, where all the investigated compounds aggregate into spherical nanoparticles. The latter, independently of the presence of bromine, demonstrate high photothermal conversion efficiency, and have been tested as photosensitizers in antibacterial photothermal therapy, highlighting the potential of self-assembled organic nanostructures based on bodipy dyes for developing new and versatile nanomaterials for photomedicine applications.