AbstractMonitoring of the human microbiome is an emerging area of diagnostics for personalized medicine. Here, the potential of different nanomaterials and nanobiosensing technologies is reviewed for the development of novel diagnostic devices for the detection and measurement of microbiome‐related biomarkers. Moreover, the current and future landscape of microbiome‐based diagnostics is defined by exploring the advantages and disadvantages of current nanotechnology‐based approaches, especially in the context of developing point‐of‐care (PoC) devices that would meet the international guidelines known as REASSURED (Real‐time connectivity; Ease of specimen collection; Affordability; Sensitivity; Specificity; User‐friendliness; Rapid & robust operation; Equipment‐free; and Deliverability). Finally, the strategies of the latest international scientific consortia working in this field are analyzed, the current microbiome diagnostics market are reported and the principal ethical, legal, and societal issues related to microbiome R&D and innovation are discussed.