Tissue engineering approaches have been adapted to reconstruct and restore functionality of impaired tissue for decades. Porous biomimetic composite scaffolds of Chitosan (CH) with hydroxyapatite (HA) for bone regeneration have also been extensively studied in the past. These porous scaffolds play a critical role in providing successful regeneration by acting as a three-dimensional template for delivering nutrients and metabolites and the removal of waste by products. The aim of the current study was to investigate in-vitro and in-vivo degradation rates of porous freeze gelated chitosan (CH) and CH hydroxyapatite scaffolds by scanning electron microscopy (SEM) to observe for morphological changes, Fourier Transform Infrared Spectroscopy (FTIR) in conjunction with photo-acoustic sampling (PAS) accessory for the analysis of chemical changes, pH analysis and UV–Vis spectroscopy of degraded supernatant. SEM results showed significant alterations in the surface morphology. FTIR-PAS spectra showed changes in the finger print region and glycosidic bonds showed signs of breakage. pH values and UV–Vis spectroscopy of the degraded supernatant were indicative of CH bonds scission in neat samples. HA incorporated specimens showed more stability. Histological sections performed after in-vivo implantation also showed greater cellular infiltration and delayed degradation profiles by HA loaded samples. Within 30 days of implantation, neat CH scaffolds showed complete in-vivo biodegradation. The current findings show the advantage of adding hydroxyapatite to porous templates which enhances hard tissue regeneration. In addition, it allows easy and cost effective fabrication of bioactive composite scaffolds.