In a previous study, we developed a computational mechanobiological model to explore the role of substrate stiffness and local oxygen availability in regulating cell fate during spontaneous osteochondral defect repair. While this model successfully simulated many aspects of the regenerative process, it was unable to predict the spatial pattern of bone formation observed during the latter stages of the repair process. The objective of this study was, therefore, to investigate the role of tissue strain in regulating the spatial and temporal patterns of stem cell differentiation during spontaneous osteochondral defect repair.Motivated by the findings of a number of prior in vitro studies, our computational mechanobiological model was updated to include rules based on the hypothesis that chondrocyte hypertrophy and endochondral ossification were inhibited in regions of high strain. The model also considered the hypothesis that excessively high magnitudes of local strain result in the formation of mechanically inferior fibrocartilage. These rules were first developed by attempting to simulate stem cell differentiation within an in vitro bioreactor system which was capable of controlling the levels of oxygen and mechanical cues within MSC-laden hydrogels. The updated model was able to predict the experimentally observed behaviour whereby the groups which were subjected to dynamic compression presented a reduction in chondrocyte hypertrophy and calcific deposition. Following this, the updated model was then used to simulate the pattern of tissue formation which had been experimentally observed during spontaneous osteochondral defect repair. As well as correctly predicting the spatial pattern of bone formation, the updated model also provided insights into the role that the mechanical environment plays on the spontaneous repair process; namely, that oxygen regulates endochondral ossification during the early phases of repair, while, during the latter stages, mechanics plays a key role in directing this process.