The present study aimed to evaluate the effect of bioactive glass as well as the presence of Ciprofloxacin drug (%Cip) into bioactive glass-chitosan composite on the in vivo behavior of these scaffolds. These scaffolds were implanted in the femoral condyl of an ovariectomized rat. The serum and organs (liver and kidney) of the under investigated rats were analyzed. Also the physicochemical properties of the prepared implants were assessed using Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction (XRD) before and after implantation (at different periods of implantation). Biochemical and histological analyses of the under investigated rats proved the biocompatibility of the prepared scaffolds. The hydroxyapatite like layer was significantly precipitated on the surface of BG-CH scaffold than BG-CH-20Cip. In this same period, FT-IR of BG-CH shows complete disappearance of Si-O-Si. Their characteristics bands were replaced by P-O group arisen form bone apatite bands. Physicochemical results show progressive degradation of BG-CH and BG-CH-20Cip that occurred at the same time as replacement of the implant by an apatite layer. However, the bioresorbability and bioactivity of BG-CH are faster than those of BG-CH-20Cip. Therefore, the incorporation of the Ciprofloxacin in the BG-CH induces a retarding effect on the formation of the hydroxyapatite, and consequently on the ossification, without any side effects on the liver-kidney.