Background During major bone substance loss, secured allogeneic bone matrix (ABM) is normally utilized for bone repair. Here, we propose a method to colonize ABM using autologous mesenchymal cells (MCs) to improve their integration. Moreover, in this study, the consequences of in vitro colonization on MCs have been evaluated. Methods After in vitro propagation of MCs, their proliferation kinetics on ABM pre-coated with gelatin, fibronectin, collagen IV and human serum (HS) was monitored, and they were compared with cells cultured without ABM for 8 weeks. The effect of ABM on cell phenotype was also assessed. Lastly, the ability of ABM-colonizing MCs to perform hematopoiesis, a function normally preserved in selected culture conditions, and their differentiation towards osteoblastic lineage were evaluated. Results MC and colony-forming unit-fibroblast proliferated 930- and 590-fold, respectively. The proliferation rate of the expanded MCs was higher, forming a 3-dimensional structure in all ABMs. Pre-coating with HS was the most efficient treatment of ABMs to increase the initial adherence of MCs, and it partly explains the reason for the higher propagation of MCs. Flow cytometry analyses revealed subtle alterations in ABM-colonizing cells; however, the ability of MCs to maintain long-term culture initiating cells proliferation and differentiate into osteoblastic lineage was preserved. Conclusions In this study, the in vitro biocompatibility of bone marrow (BM) MCs with ABMs, the role of HS in scaffold coating, and the possibility of initially using a small BM sample for this approach were demonstrated.