Bone scaffolds are 3D porous structures that facilitate tissue regeneration and rapid bone healing. The scaffolds are designed with pore sizes of 100–1000 µm to match the architecture of the cancellous bone. In present study, an electrical discharge micro-drilling (EDMD) has been used to generate a 3D porous architecture in Mg-2Zn-Mn alloy. Cylindrical scaffolds were prepared with different porosities (15 and 20%) and varying pore sizes (500 and 1000 µm). The scaffolds were coated with TiO2-HA by dip-coating method. In-vitro immersion study was carried out in Simulated Body Fluid (SBF) for a period of 7 days to observe the apatite generation and degradation of developed scaffolds. The highest mineralization with weight gain of 2.8% was observed in TiO2-HA coated scaffolds having pore size of 500 µm and porosity; 20%. The uncoated scaffold with a pore size of 1000 µm and 20% porosity has shown the highest loss of compressive strength by 10.1%, whereas the lowest strength loss of 4.3% has occurred for coated scaffold with a pore size of 500 µm and porosity of 15%. Based on the trade-off between the apatite formation and loss of mechanical integrity, the optimal pore geometry has been selected as 500 µm with a porosity of 20%.