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To date, the therapeutic efficacy of human mesenchymal stem cells (hMSCs) has been investigated in various clinical trials with moderate or, in some cases, inconsistent results. The still elusive reproducibility relates, in part, with constitutive differences in the cell preparation, translated into variable “cell potencies.” Other factors include poor cell homing and survival, and age-/disease-associated host tissue impairment. It is well accepted that within in vivo niches, MSCs exist as heterogeneous cell populations with different stemness propensities and supportive functions. Phenotype-based MSC purification of homogeneous subsets can result in cell populations with distinct biological functions. In addition, preclinical studies have shown that MSC functionalization in vitro, through cell priming, can boost their immunomodulatory, trophic, and reparative capacities in vivo. Therefore, in this review, we discuss how …