Subcutaneous implantation in a mouse can be used to investigate tissue maturation in vivo. Here we demonstrate that this simple model can recapitulate endochondral ossification associated with native skeletal development. By histological and micro-computed tomography analysis we investigated morphological changes of immature bovine osteochondral tissues over the course of subcutaneous implantation in immunocompromised mice for up to 10 weeks. We observed multiple similarities between the ectopic process and native endochondral ossification: (i) permanent cartilage retention in the upper zones; (ii) progressive loss of transient cartilage accompanied by bone formation at the interface; and (iii) remodelling of nascent endochondral bone into mature cancellous bone. Importantly, these processes were mediated by osteoclastogenesis and vascularization. Taken together, these findings advance our understanding of how the simple ectopic model can be used to study phenotypic changes associated with endochondral ossification of native and engineered osteochondral tissues in vivo.