Stem cells (SC) are among the most promising cell sources for tissue engineering due to their ability to self-renew and differentiate, properties that underpin their clinical application in tissue regeneration. As such, control of SC fate is one of the most crucial issues that needs to be fully understood to realise their tremendous potential in regenerative biology. The use of functionalized nanostructured materials (NM) to control the microscale regulation of SC has offered a number of new features and opportunities for regulating SC. However, fabricating and modifying such NM to induce specific SC response still represent a significant scientific and technological challenge. Due to their versatility, plasmas are particularly attractive for the manufacturing and modification of tailored nanostructured surfaces for stem cell control. In this review, we briefly describe the biological role of SC and the mechanisms by which they are controlled and then highlight the benefits of using a range of nanomaterials to control the fate of SC. We then discuss how plasma nanoscience research can help produce/functionalise these NMs for more effective and specific interaction with SCs. The review concludes with a perspective on the advantages and challenges of research at the intersection between plasma physics, materials science, nanoscience, and SC biology.