Allicin, the active compound of garlic extract, is a naturally sourced biomolecule, which promotes a vast range of health benefits. However, the limited stability of allicin restricts its applications in tissue engineering. Additionally, the detailed effects of allicin in bone health are yet to be explored. Our work reports on the fabrication of a novel allicin-loaded hydroxyapatite drug delivery system with enhanced biological properties. The fabricated system shows excellent antibacterial efficiency against S. aureus after 36 h of bacterial interaction with a sample. The allicin release kinetics are enhanced with polycaprolactone (PCL). The obtained results after 20 days of drug release study indicate that PCL coating leads to an increase in cumulative allicin release from ~ 35% to 70% at a physiological pH of 7.4. These scaffolds maintain stability during the whole period of drug release. Cytocompatibility of tested compositions with osteoblasts indicates enhanced cell viability and good filopodial attachment on the sample surface at day 7. These allicin-loaded antibacterial and cytocompatible scaffolds can find applications as localized delivery vehicles for bone tissue engineering.