For materials used in the production of dental and orthopedic implants or scaffolds for bone tissue regeneration, the properties such as capacity to enhance cell attachment and proliferation, and antimicrobial activity to prevent biofilm formation are very important to improve the clinical utility of the material. In this study, poly(epsilon-caprolactone) (PCL) sponges with antimicrobial activity were prepared by incorporating gentamicin loaded beta-tricalcium phosphate (beta-TCP)-Gelatin microspheres, and in vivo performances were studied. These composite systems are expected to enhance bone regeneration due to beta-TCP and prevent a possible infection by releasing gentannicin in the host location. The effects of gentamicin and beta-TCP/Gelatin microspheres in the sponge structure were studied in vivo by applying them on iliac crest defects of rabbits. Histological analyses after 8 weeks of implantation showed that the composite constructs performed significantly better in bone healing than those with antibiotic-free microspheres. Also, the PCL constructs carrying beta-TCP/Gelatin microspheres led to better bone formation than the pristine PCL scaffolds. Push-out tests demonstrated better integration of the constructs with the tissue indicating high level of material-tissue integration. This study indicates the importance of the presence of antibiotics and beta-TOP/Gelatin in the scaffolds to achieve better and faster healing in bone defects than pristine scaffolds.