Phthalocyanine derivatives have been proposed as photosensitizers for the treatment of several microbial infections. In this review, the progress in the structures of phthalocyanines was analyzed, considering that these compounds can easily functionalize and can form complexes with various metal ions. In this sense, different substituents were used to increase the interaction with the microorganisms, improving their photodynamic inactivation. Furthermore, these photosensitizers absorb strongly at phototherapeutic window, emit red fluorescence, and efficiently produce the formation of reactive oxygen species. Subsequently, the influence of binding, bacteria types, cell density, washing effect, and media on photoinactivation was remarked to elimination of microbes. Finally, photokilling of bacterial biofilm by phthalocyanines and the mechanism of action were discussed. Therefore, this review brings together the main features of phthalocyanines as antimicrobial phototherapeutic agents.