Background Despite recent advances in studies on the gastric microbiome, the role of the non‐Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM. Methods Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori‐ infection status (H. pylori‐positive and H. pylori‐negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium. Results Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori‐negative CSG, H. pylori‐negative IM, H. pylori‐negative cancer, H. pylori‐positive CSG, H. pylori‐positive IM, and H. pylori‐positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori‐negative CSG group compared to in the H. pylori‐negative IM and H. pylori‐negative cancer groups (H. pylori‐negative CSG vs H. pylori‐negative IM vs H. pylori‐negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori‐negative IM group (H. pylori‐negative CSG vs H. pylori‐negative IM vs H. pylori‐negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori‐infected stomachs progressed from gastritis to IM. In the H. pylori‐negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-. Conclusions The relative abundance of Rhizobiales was higher in patients with H. pylori‐negative IM than in those with H. pylori‐negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.