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The aim of this study was to synthesize methylene blue-incorporated quartz particles (MB@QP) and to investigate its anti-bactericidal properties. Methylene blue was incorporated inside QP and characterized for morphology and chemical structure using scanning electron microscope (SEM) and Fourier transformed infrared spectroscopy (FTIR). Specimens were randomly divided into experimental and control groups (n = 9/groups). The dentin specimen infected with Enterococcus faecalis was treated using different treatment modalities: Control groups: treatment with 5.25% of sodium hypochlorite (NaOCl) for 60 s; MB: treatment with 1 ml MB solution and incubated for 60 s; MB-PDT (photodynamic therapy): treatment with 1 ml MB solution followed by irradiation using diode laser for 60 s; MB-QP-PDT: specimens treated with MB@QP and irradiated by the diode laser for 60s, and Er,Cr:YSGG laser alone. MB@PDT therapy showed the highest efficacy in reducing the survival rate of E. faecalis (0.49%) in comparison to control NaOCl (0.78%) and Er,Cr:YSGG laser treatment (2.17%). Encapsulating MB into QP followed by the PDT significantly improved the bactericidal capacity and significantly reduced the bacterial survival rate to 0.11% (p < .05) compared to other groups. The combination of MB incorporated into QP and PDT could be an alternative treatment modality to conventional disinfection method for eliminating bacteria from the tooth dentin.