Streptococcus mutans is recognized as one of the key contributors to the dysbiotic state that results in dental caries. Existing treatment strategies reduce the incidence of tooth decay, but they also eliminate both the cariogenic and beneficial microbes. Here we introduce a novel treatment alternative using Sephadex, cross-linked dextranomer microspheres (DMs), typically used for gel filtration chromatography. In addition DM beads can be used for affinity purification of glucosyltransferases (GTFs) from S. mutans. In this study we take advantage of the native pathogenic mechanisms used by S. mutans to adhere, form a biofilm and induce dental caries through the expression of surface-associated GTFs. We demonstrate that planktonic and biofilm-grown (adhered to hydroxyapatite-coated pegs to mimic the tooth surface) S. mutans, specifically and competitively attach to DMs. Further investigation demonstrated that DMs are a specific affinity resin for S. mutans and other cariogenic/pathogenic oral streptococci, whereas other commensal and probiotic strains failed to readily adhere to DMs. Using antimicrobial cargo loaded into the DM lumen, we demonstrate that when in co-culture with non-binding to even modestly binding commensal species, S. mutans was selectively killed. This proof of concept study introduces a novel means to safely and effectively reduce the pool of S. mutans and other pathogenic streptococci in the oral cavity with limited disturbance of the necessary commensal (healthy) microbiota when compared with current oral healthcare products.