To date, no single approach to the treatment of osteochondral defects has resulted in satisfactory long-term outcomes, especially in a young and active human population. Emerging innovative tissue engineering strategies, including the use of composite scaffolds, novel cell sources and bioreactors, have shown promising results. However, these techniques need to be validated in translational animal models before they can be implemented in clinical practice. The aim of the present study was to analyse morphological and microarchitectural parameters during subchondral bone repair following transplantation of bioreactor-manufactured autologous osteochondral grafts in a sheep model. Animals were divided into 4 treatment groups: nasal chondrocyte (NC) autologous osteochondral grafts, articular chondrocyte (AC) autologous osteochondral grafts, cell-free scaffolds (CFS) and empty defects (EDs). After 6 weeks, 3 months and 12 months, bone remodelling was assessed by histology and micro-computed tomography (µCT). Although gradual remodelling and subchondral bone repair were seen in all groups across the time points, the best results were observed in the NC group. This was evidenced by the extent of new tissue formation and its best integration into the surrounding tissue in the NC group at all time points. This also suggested that nasal septum chondrocyte-seeded grafts adapted well to the biomechanical conditions of the loaded joint surface.