Regenerating or replacing bone, chondral and osteochondral defects, is an active field in tissue engineering. A general strategy is to use a temporary scaffold in which cells are seeded onto the scaffold prior to implantation or attracted into the scaffold from surrounding tissues in the implantation site to form the desired tissue. Several biomaterials have been used for the fabrication of scaffolds, including polycaprolactone (PCL) which is often used for musculoskeletal tissue engineering. The effect of the PCL scaffold architecture on the cell behavior has been investigated. However, the mechanical properties of the bulk material were not taken into account in these studies. PCL is available in a range of molecular weights, resulting in a range of bulk mechanical properties. Since bulk material stiffness is able to direct cell differentiation, it is likely that the molecular weight of PCL may influence cell behavior. Here, we investigated the bulk material properties of both low and high molecular weight PCL scaffolds fabricated through additive manufacturing. The low molecular weight PCL showed a lower bulk material stiffness. During in vitro cell culture, this resulted in a stronger tendency for hypertrophic chondrogenic differentiation compared to the high molecular weight PCL. This study shows that apart from the polymer chemistry and scaffold architecture, the bulk mechanical properties of the polymer used is an important parameter in scaffold fabrication. This is an important finding for the optimization of osteochondral tissue engineering.