Background: White spot lesions are a common adverse effect of fixed orthodontic treatment and represent the main challenge to achieving esthetic appearance. The purpose of the current study was to evaluate physico-mechanical and antimicrobial potency of orthodontic composite (OC; Transbond XT) containing nano-structured graphene oxide (nGO) (OC-nGO) as a novel composite following photodynamic therapy (PDT) and photothermal therapy (PTT) against Streptococcus mutans. Materials and methods: Following preparation of OC-nGO, shear bond strength (SBS) and adhesive remnant index (ARI) of the test OC-nGO (containing 1, 2, 5, and 10% wt. nGO) were measured using a universal testing machine and stereomicroscope, respectively. The antimicrobial activities of test OC contained different concentrations of nGO were determined by disk agar diffusion (DAD), biofilm formation inhibition, and eluted components assays. After continuously rinsed in the aging process (up to 180 days), the antimicrobial activity of OC-nGO containing the highest concentration of nGO which had simultaneously the highest antimicrobial activity and SBS value were determined by DAD, biofilm formation, metabolic activity, and gtfB gene expression assays following photo-activation using diode laser irradiation against S. mutans. Data were analyzed using One-way Analysis of Variance (ANOVA). The Bonferroni post hoc test was used for comparison between the experimental groups. The significant difference was considered at P values < 0.05. Results: OC with 5% wt. nGO showed simultaneously the highest SBS value (10.64 ± 2.76 MPa, P < 0.05) an antimicrobial and anti-biofilm activities. The OC-nGO in all test concentrations of nGO had ARI scores as same as control group (Transbond XT without the nGO) (P < 0.05). In microbial biofilm formation and gene expression assays, the reduction of photothermal disinfection and anti-virulence activities of the 5% wt. OC-nGO against test bacterium was associated with the time of aging process, so they were reduced significantly up to day 150. Diode laser irradiated 5% wt. OC-nGO suppressed 15.6 and 8.1-fold gtfB mRNA expressions in the biofilm growth of the S. mutans at days 120 and 150 of rinsing (P < 0.05). Microbial biofilm formation and gtfB gene expression in S. mutans at day 180 following PAD had a high level of similarity with OOC as the control group. 5% wt. OC-nGO following photo-activation was not colonized by the S. mutans at day 90 and significant suppressed 91.98% and 76.37% of S. mutans biofilm formation at day 120 and 150, respectively (both P < 0.05). From day 120 onwards, metabolic activity was progressively increased on laser-irradiated 5% wt. OC-nGO discs compared to the control group (OC alone). Photo-activated OC-nGO containing 5% wt. nGO suppressed 86.94% and 46.82% metabolic activity of the S. mutans at days 120 and 150 of rinsing (both P < 0.05). Conclusions: Our data support that the photo-activated 5% wt. OC-nGO can serve as an orthodontic composite/adhesive additive to control cariogenic bacterial biofilms.