In recent years, focus has moved to multiphase calcium orthophosphate scaffolds to balance the more stable calcium orthophosphate phase with another more soluble phase. This will enable the researchers to tailor the major biomedical properties to suit its intended application. In this study, beta tricalcium phosphate (β-TCP)/carbonate apatite (CO3 Ap) scaffolds were fabricated via freeze drying method. The effect of soaking time (2 h, 4 h and 6 h) on the phase transformation of β to alpha (α) phase was investigated. The scaffolds were sintered at 1300°C for respective soaking time and quenched in air to obtain biphasic β-TCP/α-TCP scaffolds. To obtain biphasic β-TCP/CO3 Ap scaffold, the obtained scaffolds were then subjected to hydrothermal treatment in 1 M of sodium bicarbonate at 200°C for 5 days for phase transformation of α-TCP phase into CO3 Ap phase via dissolution-precipitation process. X-ray diffraction (XRD) analysis before hydrothermal treatment confirms the existence of biphasic β and α phase at all soaking time. The percentage of α phase increases as soaking time increases. Fourier transform infrared (FTIR) analysis confirms the present of carbonate ions substitution into the scaffold after hydrothermal treatment. Therefore, it is concluded that as soaking time increases, the unstable phase of α-TCP increases in the biphasic β-TCP/α-TCP scaffolds. Thus, the phase transformation from α-TCP phase to CO3 Ap phase increases as soaking time increases.