Scaffolds designed for tissue engineering must consider multiple parameters, namely the permeability of the design and the wall shear stress experienced by the cells on the scaffold surface. However, these parameters are not independent from each other, with changes that improve wall shear stress, negatively impacting permeability and vice versa. This study introduces a novel multi-objective optimization framework using Direct MultiSearch (DMS) to design triply periodic minimal surface (TPMS) scaffolds for bone tissue engineering.The optimization algorithm focused on maximizing the permeability of the scaffolds and obtaining a desired value of average wall shear stress (which ranges between the values that promote osteogenic differentiation of 0.1 mPa and 10 mPa). Multiple fluid inlet velocities and target wall shear stress were analyzed. The DMS method successfully generated Pareto fronts for each configuration, enabling the selection of optimized scaffolds based on specific structural requirements.The findings reveal that increasing the target wall shear stress results in a greater number of non-dominated points on the Pareto front, highlighting a more robust optimization process. Additionally, it was also demonstrated that the tested Schwartz diamond scaffolds had a better permeability-wall shear stress relation when compared to Schoen gyroid geometries.Direct MultiSearch was proven as an effective tool to aid in the design of tissue engineering scaffolds. This adaptable optimization framework has potential applications beyond bone tissue engineering, including cartilage tissue differentiation.