Background: Scaffolds are vital for orthopedic regenerative medicine. Therefore, comprehensive studies evaluating their functionality with consideration of variable parameters are needed. The research aim was to evaluate pore geometry and scaffold porosity influence on first, cell culture efficiency in a perfusion bioreactor and second, osteogenic cell diffusion after its implantation. Methods: For the studies, five pore geometries were selected (triangular prism with a rounded and a flat profile, cube, octagonal prism, sphere) and seven porosities (up to 80%), on the basis of which 70 models were created for finite element analyses. First, scaffolds were placed inside a flow channel to estimate growth medium velocity and wall shear stress. Secondly, scaffolds were placed in a bone to evaluate osteogenic cell diffusion. Results: In terms of fluid minimal velocity (0.005 m/s) and maximal wall shear stress (100 mPa), only cubic and octagonal pores with 30% porosity and spherical pores with 20% porosity fulfilled the requirements. Spherical pores had the highest osteogenic cell diffusion efficiency for porosities up to 30%. For higher porosities, the octagonal prism’s pores gave the best results up to 80%, where no differences were noted. Conclusions: The data obtained allows for the appropriate selection of pore geometry and scaffold porosity for orthopedic regenerative medicine.