The gut microbiota (GM) is composed of >100 trillion different organisms, including bacteria, viruses, fungi, archaea and protists, coexisting in a complex system. The GM can be very sensitive to drugs, diet or even environmental pollutants. In the present review, recent data related to the interaction between the GM and heavy/toxic metals are discussed, focusing on the compounds most widely distributed in the environment or considered biopersistent. There are data to suggest that exposure to metals can alter the composition, diversity, homogeneity and structure of the GM. The specific modifications reported are not homogeneous, and a number of factors may explain this variability, including differences in metal compound, exposure modalities (e.g., food, water, in vitro), exposure time, qualitative and quantitative diversity of bacterial species in basal microbiota and analytical issues. As regards metal nanoparticles, some authors foresee the premises for a safe preventive and therapeutic use, while others have revealed harmful effects on both the gut microbiome and health. These findings, which would benefit from the application of modern approaches such as metagenomic sequencing and metabolomics, seem to indicate structural and functional analysis of gut microbiota as an early biomarker of detrimental effects from exposure to metals.