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Secondary caries often occurs at the tooth-composite margins. This study developed a novel bioactive composite containing DMAHDM (dimethylaminohexadecyl methacrylate) and NACP (nanoparticles of amorphous calcium phosphate), inhibiting caries at the enamel restoration margins in an in vitro saliva-derived biofilm secondary caries model for the first time. Four composites were tested: (1) Heliomolar nanocomposite, (2) 0% DMAHDM + 0% NACP, (3) 3% DMAHDM + 0% NACP, (D) 3% DMAHDM + 30% NACP. Saliva-derived biofilms were tested for antibacterial effects of the composites. Bovine enamel restorations were cultured with biofilms, Ca and P ion release of nanocomposite and enamel hardness at the enamel restoration margins was measured. Incorporation of DMAHDM and NACP into composite did not affect the mechanical properties (<i>p</i> > 0.05). The biofilms’ CFU (colony-forming units) were reduced by 2 logs via DMAHDM (<i>p</i> < 0.05). Ca and P ion release of the nanocomposite was increased at cariogenic low pH. Enamel hardness at the margins for DMAHDM group was 25% higher than control (<i>p</i> < 0.05). With DMAHDM + NACP, the enamel hardness was the greatest and about 50% higher than control (<i>p</i> < 0.05). Therefore, the novel composite containing DMAHDM and NACP was strongly antibacterial and inhibited enamel demineralization, resulting in enamel hardness at the margins under biofilms that approached the hardness of healthy enamel.