In this paper we developed two types of chitosan-based microspheres with and without biomimetic apatite coatings and compared their potential as injectable scaffolds for bone regeneration. The microspheres were obtained by emulsion cross-linking (E0) and coacervate precipitation (C0), respectively. They were then biomimetically coated with apatite to become E1 and C1 microspheres. The physicochemical properties and biocompatibility of the microspheres were characterized. Both E0 and C0 microspheres presented favorable ranges of diameter, density and Rockwell hardness. However, there were differences in the degree of cross-linking, shape, morphology, degradation rate, swelling rate, pH value after PBS immersion and the biocompatibility between E0 and C0. The apatite coating was successfully prepared for both C0 and E0, which enhanced the attachment, proliferation and differentiation of MC3T3-E1 cells. In conclusion, our results suggest the feasibility of using chitosan microspheres as a potential injectable scaffold. Both the preparation method and the biomimetic apatite coating contribute to their biological properties.