Abstract Secondary caries often occurs due to acids produced by biofilms at the tooth-restoration bonded interface, and is considered as one of the primary reasons for dental restoration failure. The objective of this study was (1) to synthesize nanosized EMT zeolites with silver ion exchanging, (2) to incorporate them into a commercial dental adhesive and (3) investigate the inhibition of biofilm formation at the tooth-restoration margin. The template-free zeolite nanocrystals are synthesized and stabilized in water suspensions and directly used for silver ion-exchange. Streptococcus mutans, Streptococcus gordonii, Streptococcus sanguinis were selected as representative strains of cariogenic pathogens and to form single-species biofilms. Colony-forming units (CFU), live/dead and metabolic activity were measured. The Ag+-EMT zeolites addition would not compromise the color and esthetics of dental restoration. EMT zeolites with longest exchanging time (40 min) in the adhesives achieved the greatest reduction in early attachment, bacterial biomass, biofilm growth and metabolic activity. Biofilm CFU counts were reduced by nearly 2 orders of magnitude for all three cariogenic pathogens. Therefore, the adhesives containing Ag+ exchanged zeolites had remarkable antibacterial properties to serve as “bioactive” adhesive materials and revealed its potential value for anti-biofilm and anti-caries clinical applications.