The role of intestinal Prevotella species in human health is controversial, with both positive and negative associations. Strain-level diversity may contribute to discrepancies in genus and species associations with health and disease. We dissected the gut metagenomes of Italians with varying dietary habits, investigating the presence of distinct Prevotella copri strains. Fiber-rich diets were linked to P. copri types with enhanced potential for carbohydrate catabolism. P. copri strains associated with an omnivore diet had a higher prevalence of the leuB gene—involved in branched-chain amino acid biosynthesis—a risk factor for glucose intolerance and type 2 diabetes. These P. copri pangenomes were compared to existing cohorts, providing evidence of distinct gene repertoires characterizing different P. copri populations, with drug metabolism and complex carbohydrate degradation significantly associated with Western and non-Western individuals, respectively. Strain-level P. copri diversity in gut microbiomes is affected by diet and should be considered when examining host-microbe associations. Display omitted •Screening of human gut metagenomes reveals different Prevotella copri pangenomes•Habitual diet and lifestyle can select different P. copri strains•Strains from non-Western subjects show higher potential for complex fiber break-down•Strains from Western subjects have a higher prevalence of drug metabolism genes The gut microbiome includes several strains per species, with high genomic diversity. By examining Italian subjects with varying dietary habits, De Filippis et al. demonstrate that diet may select distinctive Prevotella copri strains with distinguishable functions. This diversity may explain subject-specific responses to dietary interventions and variations in human health.