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This study evaluated the efficacy of experimental TEGDMA-functionalized dicalcium phosphate dihydrate (T-DCPD) filler-based resin-based composites (RBC) in preventing caries lesions around the restoration margins (secondary caries, SC). Standardized Class-II cavities were made in sound molars with the cervical margin in dentin. Cavities were filled with a commercial resin-modified glass-ionomer cement (RMGIC) or experimental RBCs containing a bisGMA-TEGDMA resin blend and one of the following inorganic fractions: 60 wt.% Ba glass (RBC-0); 40 wt.% Ba glass and 20 wt.% T-DCPD (RBC-20); or 20 wt.% Ba glass and 40 wt.% T-DCPD (RBC-40). An open-system bioreactor produced Streptococcus mutans biofilm-driven SC. Specimens were scanned using micro-CT to evaluate demineralization depths. Scanning electron microscopy and energy-dispersive X-ray spectroscopy characterized the specimen surfaces, and antimicrobial activity, buffering effect, and ion uptake by the biofilms were also evaluated. ANOVA and Tukey’s tests were applied at p < 0.05. RBC-0 and RBC-20 showed SC development in dentin, while RBC-40 and RMGIC significantly reduced the lesion depth at the restoration margin (p < 0.0001). Initial enamel demineralization could be observed only around the RBC-0 and RBC-20 restorations. Direct antibiofilm activity can explain SC reduction by RMGIC, whereas a buffering effect on the acidogenicity of biofilm can explain the behavior of RBC-40. Experimental RBC with CaP-releasing functionalized T-DCPD filler could prevent SC with the same efficacy as F-releasing materials.