The study of the human microbiome is a multidisciplinary area that affects from the field of technology to that of personalized medicine. The possibility of using microbiota biomarkers for the improvement in the diagnosis and monitoring of diseases (e.g. cancer), health conditions (e.g. obesity) or clinical parameters (e.g. ageing) has aroused great expectations, also in the scope of bio-electroanalytical chemistry. The well-known advantages of electrochemical transduction: high sensitivity, rapid response and possibility of miniaturization, together with the potential of new nanomaterials to improve both the design of electrode platforms and the performance of the resulting electrochemical biosensors make presumably a huge development in the next few years providing a better understanding of human microbiome entities. In this review article, the recent applications of electrochemical (bio)sensors for monitoring microbial metabolites and biomarkers of diseases related to different types of the human microbiome, with a special focus on the gastrointestinal microbiome, are reviewed. Examples of electrochemical devices applied to real samples are critically discussed as well as the challenges and prospects to be faced.