New tetrasubstituted zinc (II) and indium (III) phthalocyanines bearing dimethylamino chalcone group (complexes 3 and 4) as well as their quaternized analogs (3a and 4a) have been assessed for their photodynamic therapy (PDT) of cancer as well as photodynamic antimicrobial chemotherapy activities against biofilms and planktonic cultures of pathogenic bacteria of Staphylococcus aureus and Escherichia coli. Compared to the non-quaternized phthalocyanines 3 and 4, the cationic phthalocyanines 3a and 4a exhibit a higher photodynamic inactivation against the planktonic cells with log reduction values above 9 at a concentration of 1.25 µM. This was attributed to the positive charge which enhances cellular uptake. More interestingly, 3a and 4a show a higher photodynamic inactivation (less than 3% of S. aureus survived) on their biofilm counterparts thanks to their stronger affinity to these cells. 3a and 4a Pcs also exhibited interesting PDT activity against MCF-7 cancer cells giving IC50 values of 17.9 and 7.4 μM, respectively following 15 min irradiation. The obtained results in this work show that the positively charged phthalocyanines 3a and 4a are potential antibacterial photosensitizers that show some selectivity toward the Gram-positive and Gram-negative bacteria as well as MCF-7 breasts cancer cells.