Spinal cord injury (SCI) is a trauma that results in loss of function below the site of injury. Additionally, SCI induces systemic inflammation, which is in part responsible of brain dysfunction. Currently, many therapeutic approaches have been carried out. In particular, transplantation of bulbar olfactory ensheathing cells (bOECs) has shown therapeutic effects in mice and, to a lesser extent, in humans. Given these observations, we wondered about the effect of the lesion on the quality of the transplanted therapeutic material when cells are harvested after SCI. First, the effects of SCI on bOECs in primary culture were investigated. The results show that SCI induced a major change of in vitro RNA expression in bOECs primary culture. Then, to compare the therapeutic effects of OECs from healthy (bOECs H) and injured (bOECs I) mice, Th9 SCI was performed on mice and cells were transplanted. On these animals, functional analyses and immunochemical experiments were performed to analyze cellular reactivity and tissue regeneration. Our results demonstrate that, after transplantation, the bOECs I group showed poorer functional recovery compared to the bOECs H group, associated with a larger spinal scar composed of less permissive extracellular matrix. These differences seem to be correlated to a lower reactivity of microglial cells in the presence of bOECs H. Altogether, this study shows that SCI reduces the therapeutic capacity of bOECs. These results are particularly interesting in the context of the future clinical use of these cell transplants for SCI patients.