In this study, a porous chitosan-organically modified montmorillonite-hydroxyapatite (CS-OM-HA) composite scaffold was developed by combining microwave irradiation and gas foaming method. Hydroxyapatite (HA) particles of size ∼ 65 nm were synthesized and characterized by X-ray diffraction (XRD) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. The prepared composite scaffolds were characterized using ATR-FTIR, XRD, mercury intrusion porosimeter (MIP) and scanning electron microscopy (SEM) studies. The synergistic effect of HA and OM on the mechanical and in vitro biological properties (swelling, degradation, protein adsorption and bioactivity) of the composite scaffolds were evaluated. Swelling, degradation, mechanical property, bioactivity and protein adsorption studies of CS-OM-HA composite scaffolds have shown desirable results in comparison with the pure CS and CS-OM composite scaffolds. CS-OM-HA composite scaffolds were also found to be non-cytotoxic to MG 63 osteoblast cell lines. From the study, it can be concluded that the novel CS-OM-HA composite scaffold with improved mechanical and in vitro biological properties has wide potential in non-load bearing bone tissue engineering applications.