Omics strategies have triggered a revolution in the understanding of the microorganisms that reside in our body, and their implications in health and disease. For diagnosis and therapeutics, metabolomic fingerprinting is the most powerful approach, since the metabolites represent the actual interplay between humans and microbes. Studying the metabolome requires several new high-throughput analytical techniques and innovative computational methodologies. Herein, we will focus on the metabolomics workflow for gut microbiota analysis, including sampling, laboratory procedures, and available analytical techniques, paying special attention to microbiota isolation and multiplatform complementarity. Finally, we will summarize some applications and implications of gut microbiota metabolites in biomarkers discovery and several therapeutic strategies, such as fecal microbiota transplantation and the usage of prebiotics and probiotics.