The growing resistance to antibiotics has rendered antimicrobial photodynamic inactivation (PDI) an attractive alternative treatment modality for infectious diseases. Chitosan (CS) was shown to further potentiate the PDI effect of photosensitizers and was therefore used in this study to investigate its ability to potentiate the activity of erythrosine (ER) against bacteria and yeast. CS nanoparticles loaded with ER were prepared by ionic gelation method and tested for their PDI efficacy on planktonic cells and biofilms of Streptococcus mutans, Pseudomonas aeruginosa and Candida albicans. The nanoparticles were characterized for their size, polydispersity index and zeta potential. No toxicity was observed when planktonic cells and biofilms were treated with the nanoparticles in the dark. However, when the cells were exposed to light irradiation after treatment with free ER or ER/CS nanoparticles, a significant phototoxicity was observed. The antimicrobial activity of ER/CS nanoparticles was significantly higher than ER in free form. The particle size and incubation time of the nanoparticles also appeared to be important factors affecting their PDI activity against S. mutans and C. albicans.