(1) Background: This study compares the antibacterial effect of coated and impregnated flexible dentures with magnesium oxide nanoparticles (MgONPs) against Streptococcus mutans. (2) Methods: the study used flexible denture material discs. The experimental groups were uncoated dics (control), 5% MgONPs coated discs (coated), and 5% MgONPs impregnated discs (impregnated). The homogenous distribution of MgONPs within the matrix was determined using scanning electron microscopy (SEM), and surface roughness and modulus elasticity were also measured. The antibacterial efficacy was tested against Streptococcus mutans in suspension and biofilm. The adhesion of microorganisms was assessed using an adherence assay test, optical light microscopy, and turbidity test. (3) Results: The nanoparticles were successfully coated or impregnated on the substrate and caused a significant increase in roughness. The effect of 5% MgONPs was significant (p < 0.05). The flexible denture samples whether coated or impregnated with 5% MgONPs effectively inhibited the growth of microorganisms. The Streptococcus mutans growth was 2.5 folds higher in control compared to coated samples, while Streptococcus mutans growth was 1.5 folds higher in control compared to impregnated samples. Furthermore, this study confirmed there was a homogenous distribution of MgONPs for both coated and impregnated groups. (4) Conclusions: It was found that addition of 5% MgONPs can prevent the attachment of Streptococcusn mutans to flexible removable denture material. Additionally, the antibacterial effect was higher in the coated-samples compared to impregnated-samples.