A series of silicon(IV) phthalocyanines axially substituted with methylparaben, ethylparaben, propylparaben and butylparaben groups were synthesized and studied as photosensitizers for antimicrobial photodynamic therapy. The absorption, fluorescence, photodegradation and singlet oxygen generation properties of the synthesized Si(IV) phthalocyanines were studied. In vitro antibacterial photodynamic therapy was investigated against cariogenic pathogenic bacterium Streptococcus mutans. Axially propylparaben substituted Si(IV) phthalocyanine showed significant photodynamic efficacy (log 4) at concentration of 10 μM and mild irradiation (60 mW cm−2, 50 J cm−2, LED 637 nm). The low inactivation capacity was observed for the other studied Si(IV) phthalocyanines. The uptake and localization properties of axially propylparaben substituted Si(IV) phthalocyanine showed a sufficient level of accumulation in planktonic cultured bacterium and a complete penetration depth into the biomass of the 48-h bacterial biofilm.