Background Gastritis is characterized by alterations in the gastric microbiota. This dysbiosis in the stomach may affect immune system regulation as well as influence the oral microbiota. Periodontal disease results from dysbiosis of subgingival microbial communities that cause inflammatory responses in periodontal tissues. The aim of our study is to examine the oral flora profile and dysbiosis status of gastritis patients along with their periodontal status.Methods A total of 30 patients were included in our study, divided into two groups 15 patients diagnosed with gastritis and 15 systemically healthy individuals. Subsequently, the patients were subdivided into subgroups as periodontally healthy, gingivitis, and stage 1 periodontitis based on their periodontal status. Clinical periodontal parameters and saliva samples were collected. The microbial flora was analyzed using metagenomic analysis through next-generation sequencing methods. Clinical and microbiological parameters were evaluated using non-parametric statistical methods.Results While no differences were observed in any metric in beta diversity analysis across gender groups, study groups, and subgroups, bacterial diversity was found to be higher in women in the Simpson, Shannon and Chao1 metrics in alpha diversity analysis, In the subgroups, a significant increase was observed in the stage 1 periodontitis-gastritis group in the Chao1 metric. Bacterial taxa that showed statistically significant differences between the groups and subgroups were identified using LEfSe analysis.Conclusion Our study underscore dysbiosis in the oral flora in the context of gastritis while also taking into account the periodontal status. Gastritis with periodontitis may enhance the microbial diversity and density. Future research studies are needed to unravel systemic interaction between periodontitits and gastritis.Trial Registration: This clinical trial was registered at ClinicTrials.gov (NCT07378540) Registeration Date: 29/01/2026.