The global rise in antibiotic resistance among oral pathogens necessitates exploring natural and innovative alternatives for dental caries management. This study aimed to synthesize, characterize, and evaluate a novel clove extract-loaded nano-hydroxyapatite composite (nHA-CE) for its dual functionality: biomimetic remineralization and enhanced antimicrobial activity against dental caries-associated microbes. Nano-hydroxyapatite (nHA) was synthesized via wet chemical precipitation and characterized using XRD, FTIR, AFM, and DLS. Clove extract was obtained by ethanolic extraction and analyzed by GC-MS. The nHA-CE composite was prepared, and its antibacterial efficacy was tested against oral pathogens using agar well diffusion and compared to standard antibiotics. The nHA particles were spherical, with an average size of ~ 80 nm. Eugenol (72.5%) was the major component in clove extract. The nHA-CE composite showed significantly larger inhibition zones against all pathogens, especially Streptococcus mutans (50 ± 0.8 mm), outperforming conventional antibiotics. The composite also exhibited sustained eugenol release and maintained stability over 30 days. The nHA-CE composite is a promising biomaterial for dental caries prevention, combining effective remineralization with potent, broad-spectrum antimicrobial activity, offering a natural alternative to conventional treatments.