The objectives of this study were to: (1) develop a new bioactive dental bonding agent with nanoparticles of amorphous calcium phosphate and dimethylaminohexadecyl methacrylate for tooth root caries restorations and endodontic applications, and (2) investigate biofilm inhibition by the bioactive bonding agent against eight species of periodontal and endodontic pathogens for the first time. Bonding agent was formulated with 5 % of dimethylaminohexadecyl methacrylate. Nanoparticles of amorphous calcium phosphate at 30 wt% was mixed into adhesive. Eight species of biofilms were grown on resins: Porphyromonas gingivalis, Prevotella intermedia, Prevotella nigrescens, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Parvimonas micra, Enterococcus faecalis, Enterococcus faecium. Colony-forming units, live/dead assay, biomass, metabolic activity and polysaccharide of biofilms were determined. The results showed that adding dimethylaminohexadecyl methacrylate and nanoparticles of amorphous calcium phosphate into bonding agent did not decrease dentin bond strength (P > 0.1). Adding dimethylaminohexadecyl methacrylate reduced the colony-forming units of all eight species of biofilms by nearly three orders of magnitude. The killing efficacy of dimethylaminohexadecyl methacrylate resin was: P. gingivalis > A. actinomycetemcomitans > P. intermedia > P. nigrescens > F. nucleatum > P. micra > E. faecalis > E. faecium. Dimethylaminohexadecyl methacrylate resin had much less biomass, metabolic activity and polysaccharide of biofilms than those without dimethylaminohexadecyl methacrylate (P < 0.05). In conclusion, a novel dental adhesive was developed for root caries and endodontic applications, showing potent inhibition of biofilms of eight species of periodontal and endodontic pathogens, and reducing colony-forming units by three orders of magnitude. The bioactive adhesive is promising for tooth root restorations to provide subgingival margins with anti-periodontal pathogen capabilities, and for endodontic sealer applications to combat endodontic biofilms.