The tendon-bone junction (TBJ) is a unique, mechanically dynamic, structurally graded anatomical zone which transmits tensile loads between tendon and bone. Current surgical repair techniques rely on mechanical fixation and can result in high re-failure rates. We have recently described a new class of collagen biomaterial that contains discrete mineralized and structurally aligned regions linked by a continuous interface to mimic the graded osteotendinous insertion. Here we report the combined influence of graded biomaterial environment and increasing levels of applied strain (0 – 20%) on MSC orientation and alignment. In osteotendinous scaffolds, which contain opposing gradients of mineral content and structural alignment characteristic of the native osteotendinous interface, MSC nuclear and actin alignment was initially dictated by the local pore architecture, while applied tensile strain enhanced cell alignment in the direction of strain. Comparatively, in layered scaffolds that did not contain any structural alignment cues, MSCs were randomly oriented in the unstrained condition, then became oriented in a direction perpendicular to applied strain. These findings provide an initial understanding of how scaffold architecture can provide significant, potentially competitive, feedback influencing MSC orientation under applied strain, and forms the basis for future tissue engineering efforts to regenerate the osteotendinous enthesis.