The combination of mesenchymal stem cells (MSCs) and biomimetic matrices for cell-based therapies has led to enormous advances, including the field of cell microencapsulation technology. In the present work, we have evaluated the potential of genetically modified MSCs from mice bone marrow, D1-MSCs, immobilized in alginate microcapsules with different RGD (Arg-Gly-Asp) densities. Results demonstrated that the microcapsules represent a suitable platform for D1-MSC encapsulation since cell immobilization into alginate matrices does not affect their main characteristics. The in vitro study showed a higher activity of D1-MSCs when they are immobilized in RGD-modified alginate microcapsules, obtaining the highest therapeutic factor secretion with low and intermediate densities of the bioactive molecule. In addition, the inclusion of RGD increased the differentiation potential of immobilized cells upon specific induction. However, subcutaneous implantation did not induce differentiation of D1-MSCs toward any lineage remaining at an undifferentiated state in vivo.