Computational methods were combined with an experimental setup in order to investigate the response of human umbilical cord stem cells to 3D electrospun and printed scaffolds, when dynamically stimulated in a bioreactor. Key parameters associated to bioreactor working conditions were computationally investigated using Comsol software to use the output for the planned experimental setup. Based on the theoretical observations, the influence of the inlet velocity, cell number, and exposure time in the bioreactor were analyzed and the in vitro parameters were adjusted accordingly. MSCs were seeded in different numbers in the 3D porous scaffolds and stimulated in the bioreactor (0.5 and 2 h duration, 3 and 6 mm/s inlet velocity). Polycaprolactone 3D electrospun, and polyurethane and polylactic acid 3D-printed scaffolds were fabricated and fibronectin-coated. The computational study predicted initial events in the process of cells deposition and attachment. Total protein, osteopontin, and osteocalcin levels in cells deposited in scaffolds were investigated; SEM and confocal imaging confirmed the biomarker analysis. MSCs proliferated well in PCL. Polyurethane enabled extremely rapid proliferation followed by differentiation, while PLA induced a moderate proliferation and parallel mineralization. The scaffolds stiffness has been found as the key enabling parameter decisive for cells feedback.