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This study set out to develop a biomimetic scaffold by incorporating osteoinductive hydroxyapatite (HA) particles into a porous alginate gel matrix via a cell-friendly pathway. Two types of alginate/calcium phosphate (Alg/CP) composites were prepared through alkaline phosphatase (ALP) mediated mineralization and counter-diffusion precipitation. Structural characteristics were analyzed by scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM). Thermal stability and mineral content were studied by means of thermogravimetric (TG) analysis. X-ray diffraction (XRD) and Rietveld refinement showed the presence of bone-like hydroxyapatite. Our studies suggested that the gradual nature of enzymatic process together with alginate matrices provide regulation of nanocrystalline hydroxyapatite formation. The ALP-mediated mineralization process has great advantages over counter-diffusion precipitation, providing homogenous mineral distributions, smaller crystal sizes, and increased apparent Young's moduli, which creates a better structure for bone defect repair scaffolds.