Mesenchymal stem cells (MSC) are present in all organs and tissues. Several studies have shown the therapeutic potential effect of MSC or their derived products. However, the functional heterogeneity of MSC constitutes an important barrier for transferring these capabilities to the clinic. MSC heterogeneity depends on their origin (biological niche) or the conditions of potential donors (age, diseases or unknown factors). It is accepted that many culture conditions of the artificial niche to which they are subjected, such as O 2 tension, substrate and extracellular matrix cues, inflammatory stimuli or genetic manipulations can influence their resulting phenotype. Therefore, to attain a more personalized and precise medicine, a correct selection of MSC is mandatory, based on their functional potential, as well as the need to integrate all the existing information to achieve an optimal improvement of MSC features in the artificial niche. Keywords Regenerative medicine • Aging diseases • Diabetes • Lupus • Secretome • Conditioned medium • Extracellular vesicles • Exosomes Abbreviations 2D Two-dimensional 3D Three-dimensional AD Adipose-derived AD-MSC Adipose-derived mesenchymal stem cell Ad-FKN Adenoviral vector fractalkine gene BM Bone marrow BM-MSC Bone marrow-derived mesenchymal stem cell bBM-MSC Bovine bone marrow-derived mesenchymal stem cell BNDF Brain-derived neurotrophic factor CD Cluster of differentiation cGMP Current good manufacturing practice Cellular and Molecular Life Sciences Luis A. Costa and Noemi Eiro contributed equally to this work.