This chapter investigates the convergence of ethical considerations and regulatory frameworks within the rapidly developing area of microbiota-based precision medicine. As microbiome therapies draw more attention, it is essential to comprehend the consequences of their development and commercialization. Ethical considerations including health disparities and informed consent are of utmost importance, especially considering the disproportionate representation of specific ancestries in current research, which could worsen inequities in access to healthcare. However, the regulatory perspective also has many problems to consider concerning efficacy and safety-not just of fecal microbiota transplantation, but also that of other microbiome interventions. This chapter also discusses the role of the microbiome in affecting pharmacokinetics and variability in drug response, and identifies the need for multi-dimensional strategies that incorporate both microbiota and genetic signals. Eventually, responsible advancement of precision medicine based on microbiota will depend upon the resolution of these multi-dimensional challenges.