Adipose-derived mesenchymal stem cells (ADSCs) and bone marrow-derived mesenchymal stem cells (BMSCs) have shown great potential in clinical applications. However, the similarities and differences between these two cell types have not been fully elucidated. Recent advances in transcriptomic and metabolomic research have provided valuable insight into the characteristics and functions of ADSCs and BMSCs. In this perspective article, we review the key findings from these studies, including cellular heterogeneity as well as differences in metabolic and secretory properties. We discuss how these insights can help guide the selection of the most suitable cell source for the clinic, and the optimization of preconditioning strategies prior to clinical deployment. Furthermore, we analyze the current landscape of products and clinical trials involving ADSCs and BMSCs, highlighting their therapeutic potential. We propose that the integration of multi-omics datasets will be crucial for establishing a comprehensive understanding of ADSC and BMSC identity and potency, and the provision of quality-assured stem cell-derived products for the clinic.