Composites of hydroxyapatite (HAp) and organic polymers have been widely utilized as porous scaffold materials for bone tissue engineering. Chitosan is feasible for compositing with HAp because of its biodegradability, high biocompatibility and antimicrobial activity. We previously developed chemical cross-linker-free chitosan-based cryosponges by freeze-thawing aqueous solutions of chitosan-gluconic acid conjugate (CG). In this study, CG cryosponges were coated with HAp by an alternating soaking method to prepare HAp/CG composite scaffolds. With 1 soaking cycle, scaffolds possessed open pore structures and a skeletal surface coated with HAp particles. The Ca/P atomic ratio of HAp in these scaffolds was within the range of normal human adult skeletal bones. Further, scaffolds showed minimal cytotoxicity towards a human osteosarcoma cell line and did not induce necrosis in the surrounding tissue after subcutaneous implantation in mice. Our results demonstrate that HAp/CG composite scaffolds prepared with a single cycle of soaking are potentially useful for bone regeneration.