Histidine is an essential amino acid that must be obtained from the diet in humans. It plays a key role in anti-inflammatory functions and also serves as an energy source for the gut microbiota. Disrupted histidine metabolism and altered histidine-related metabolites have been implicated in a wide spectrum of metabolic and inflammatory disease outcomes, including type 2 diabetes, diverticulitis, inflammatory bowel disease, and liver cancer. However, the detailed relative contributions of food sources and the gut microbiome to histidine-related metabolites remain unclear. We analyzed stool shotgun metagenomic and untargeted metabolomic data among 226 participants from the Microbiome among Nurses (Micro-N) cohort in the Nurses’ Health Study II and examined associations of diet (34 food groups, 3 dietary patterns, 10 nutrients) and 383 microbiome species with 11 histidine-related metabolites. As expected, fecal metabolites were generally well-correlated with gut microbial composition. For example, Clostridiaceae members (e.g. Clostridium symbiosum and Clostridiales bacterium) and Ruminococcus gnavus were strongly positively correlated (ρ>0.2, FDR-adjusted p<0.05) with most histidine-related metabolites, except for a strong negative correlation (ρ<-0.4, FDR-adjusted p<0.0001) with urocanic acid. In contrast, the Lachnospiraceae family (e.g., Lachnospiraceae bacterium and Lachnospira eligens) and Eubacterium siraeum displayed opposite correlation patterns with these metabolites (ρ<-0.2, FDR-adjusted p<0.0001 with most metabolites; ρ>0.2, FDR-adjusted p<0.0001 with urocanic acid). These association patterns aligned with previous studies on the regulation of histidine metabolism genes identified across microbial species. Conversely, there were generally modest correlations between dietary features and the fecal levels of histidine-related metabolites, except for a significant positive correlation (ρ=0.2, FDR-adjusted p=0.08) between liquor consumption and 1-methylhistamine, consistent with prior findings of elevated circulating 1-methylhistamine among alcohol drinkers. This study demonstrated the relative contributions of the microbiome and diet to histidine-related metabolites in the gut and identified key microbial species linked to these metabolites. These findings highlight the need to further explore the role of diet and the gut microbiome in histidine-related metabolic disturbances and health conditions.