Stem cell differentiation is known to be influenced by the mechanical properties of the surrounding extracellular matrix (ECM); however, little is known about the mechanical phenotypes of differentiating stem cells within the ECM. Here, this study uses osteoinductive, ECM-mimetic peptide nanofibers to investigate the changes in the mechanical properties of rat mesenchymal stem cells (rMSCs) during osteogenic differentiation. In addition, octafluorocyclobutane (C4F8)-coated atomic force microscopy (AFM) cantilevers are developed to minimize tip–sample adhesion during the nanomechanical characterization of rMSCs, and osteogenic differentiation is monitored through molecular analysis in conjunction with AFM measurements. rMSCs cultured on osteoinductive peptide nanofibers differentiate at substantially higher rates, form osteogenic cell clusters, deposit calcium to the surrounding matrix, and strikingly increase their Young's moduli throughout the osteogenic differentiation process compared to controls. These results show that the elasticity profiles of differentiating rMSCs may change significantly depending on environmental factors and especially the degree of biomineralization, and that the natural elasticity responses of cells cultured on scaffolds may be considerably different from those observed on non-bioactive surfaces. This is important for the identification of cell elasticity as a biophysical marker of osteogenic differentiation of MSCs, and indicates that biomineralization might have a predominant role on cell mechanics.