Introduction Chronic infection with Helicobacter pylori (Hp) is an essential cause of gastrointestinal pathologies in adults. Despite being a microorganism proven to play a role in vitamin B12 deficiency by causing gastric atrophy, Hp's role in patients with non-atrophic gastritis has not been fully explained. Our study investigated whether the presence and density of Hp is related to vitamin B12 and folate deficiencies in patients with non-atrophic gastritis. Methods This retrospective cohort study analyzed the following parameters, vitamin B12, folate, and mean red blood cell volume (MCV) in the hemogram; these were measured simultaneously in patients diagnosed with non-atrophic gastritis who had undergone gastroscopy to investigate Hp levels. Patients with conditions that could have caused vitamin B12 and folate deficiencies were excluded from the study. The study included 244 patients who met the criteria. The Sydney classification was used for histopathologic grading and staging of gastric biopsies of patients with gastritis. Results There was no relationship between the presence and density of Hp with vitamin B12 levels. However, folate levels were significantly lower in Hp-positive patients than in Hp-negative patients (p = 0.017). Folate levels were substantially lower in patients with chronic pan-mucosal gastritis than in patients with chronic inactive gastritis (p = 0.034). Statistically, a significant difference was found between folate levels on the basis of neutrophil activity and inflammation score (p = 0.011 and p <0.001, respectively). Conclusions Although there was no statistically significant relationship between the presence and density of Hp and vitamin B12, our study found an association between folate levels and Hp density. This may be associated with the time for the depletion of vitamin B12 and folate stores and the relatively early stage of gastritis. In cases with vitamin B12 and folate deficiencies, appropriate studies should be performed for specific epidemiological reasons in respective fields.