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Flowable resins used for dental restoration are subject to biofilm formation. Zinc has antibacterial properties. Thus, we prepared a zinc-doped phosphate-based glass (Zn-PBG) to dope a flowable resin and evaluated the antibacterial activity of the composite against Streptococcus mutans (S. mutans) to extrapolate the preventative effect toward secondary caries. The composites were prepared having 0 (control), 1.9, 3.8, and 5.4 wt.% Zn-PBG. The flexural strength, elastic modulus, microhardness, depth of cure, ion release, inhibition zone size, and number of colony-forming units were evaluated and analyzed using ANOVA. The flexural strength of the control was significantly higher than those of Zn-PBG samples (p < 0.05). However, all samples meet the International Standard, ISO 4049. The microhardness was not significantly different for the control group and 1.9 and 3.8 wt.% groups, but the 5.4 wt.% Zn-PBG group had a significantly lower microhardness (p < 0.05). Further, the composite resins increasingly released P, Ca, Na, and Zn ions with an increase in Zn-PBG content (p < 0.05). The colony-forming unit count revealed a significant reduction in S. mutans viability (p < 0.05) with increase in Zn-PBG content. Therefore, the addition of Zn-PBG to flowable composite resins enhances antibacterial activity and could aid the prevention of secondary caries.