Cell biomechanics plays a major role as a promising biomarker for early cancer diagnosis and prognosis. In the present study, alterations in modulus of elasticity, cell membrane roughness, and migratory potential of MCF-7 (ER+) and SKBR-3 (HER2+) cancer cells were elucidated prior to and post treatment with conditioned medium from human umbilical mesenchymal stem cells (hUMSCs-CM) during static and dynamic cell culture. Moreover, the therapeutic potency of hUMSCs-CM on cancer cell’s viability, migratory potential, and F-actin quantified intensity was addressed in 2D surfaces and 3D scaffolds. Interestingly, alterations in ER+ cancer cells showed a positive effect of treatment upon limiting cell viability, motility, and potential for migration. Moreover, increased post treatment cell stiffness indicated rigid cancer cells with confined cell movement and cytoskeletal alterations with restricted lamellipodia formation, which enhanced these results. On the contrary, the cell viability and the migratory potential were not confined post treatment with hUMSCs-CM on HER2+ cells, possibly due to their intrinsic aggressiveness. The increased post treatment cell viability and the decreased cell stiffness indicated an increased potency for cell movement. Hence, the therapy had no efficacy on HER2+ cells.