Mesenchymal stem cells (MSCs) are multipotent progenitor cells with the ability to differentiate into several cell types that hold great promise for therapeutic applications. However, the maintenance of proliferative and stemness capacity following in vitro expansion remains a significant challenge. Triiodothyronine (T3) plays a crucial role in embryogenesis and fetal development, yet the knowledge of its effects on MSCs’ survival and function is limited. Here, we investigate the impact of T3 treatment in bone marrow (BM)-MSCs and adipose tissue (AT)-MSCs isolated from C57BL/6J mice, to assess stemness preservation, proliferation, and gene expression during in vitro expansion. To this end, MSCs were treated with T3 at various concentrations for 24 and 48 h, and thyroid hormone-responsive and stemness-related genes expression, proliferation, clonogenic potential, and surface marker profiles were analyzed using reverse transcript quantitative PCR, Cell Counting Kit-8, colony-forming unit-fibroblast assays, and flow cytometry. Our results show that T3 exposure did not affect variability or clonogenic potential of BM-MSCs and AT-MSCs, and the expression of T3-responsive genes is activated by distinct time- and dose-dependent responses to T3 in AT-MSCs and BM-MSCs. However, in BM-MSCs, a transient increase in pluripotent markers was observed. Conversely, AT-MSCs exhibited sustained increases in Nano-g, Sca-1, and Ssea-1, particularly at 10 and 100 nM. Collectively, we observed that T3 exposure during in vitro expansion enhanced stemness features in MSCs. This finding was more prominent in AT-MSCs compared with BM-MSCs. The data suggest that T3 exposure during AT-MSCs expansion could be a valuable tool to increase the yield and stemness of these MSCs, facilitating their therapeutic use.