Stable surface modifications of polydimethylsiloxane (PDMS) are of crucial importance for the exploitation of the versatile physical properties of silicone in many biological applications. Surface hydrophobic recovery in fact poses severe time limitations to the observation of biological events and, in particular, to cell culturing. A novel method of stable modification of PDMS surface chemistry was therefore elaborated, relying on the use of genipin as a natural low-toxicity cross-linker, and involving free amine moieties. Its effectiveness to long-term cultures was studied by preparation of thin PDMS films with different stiffness. After assessment of surface chemistry and substrate stiffness, H9c2 muscle cells were cultured on the modified films, and differentiating myoblasts were observed for a period of four weeks since differentiation induction. A lower PDMS stiffness increased myotube width and supported a higher actin and myosin colocalization within myotubes, suggesting the achievement of myotube functional maturity. These results provide evidence of the effectiveness of the proposed procedures to PDMS surface chemistry modification. Furthermore, modified PDMS membranes prove to be suitable to several long-term studies of cell behaviour in vitro, including muscle cell contractility investigations.