Regenerative medicine is a novel clinical branch aiming at the cure of diseases by replacement of damaged tissues. The crucial use of stem cells makes this area rich of challenges, given the poorly understood mechanisms of differentiation. One highly needed and yet unavailable technology should allow us to monitor the exact (metabolic) state of stem cells differentiation to maximize the effectiveness of their implant in vivo. This is challenged by the fact that not all relevant metabolites in stem cells differentiation are known and not all metabolites can currently be continuously monitored. To bring advancements in this direction, we propose the enhancement and integration of two available technologies into a general pipeline. Namely, high-throughput biochip for gene expression screening to pre-select the variables that are most likely to be relevant in the identification of the stem cells’ state and low-throughput biochip for continuous monitor- ing of cell metabolism with highly sensitive carbon nanotubes-based sensors. Intriguingly, additionally to the involvement of multidisciplinary expertise (medi- cine, molecular biology, computer science, engineer- ing, and physics), this whole query heavily relies on biochips: it starts in fact from the use of high- throughput ones, which output, in turn, becomes the base for the design of low-throughput, highly sensitive biochips. Future research is warranted in this direction to develop and validated the proposed device.