The relation between salt intake and intestinal metaplasia (IM) types and the potential interaction with H. pylori virulence are poorly understood and may contribute to further understand gastric carcinogenesis. We quantified the association between dietary salt exposure and complete, incomplete, and mixed IM, taking into account the potential effect modification according to the virulence of H. pylori infecting strains. H. pylori-infected male volunteers (n = 233) underwent an upper digestive endoscopy and completed questionnaires comprising different measures of salt exposure (main food items/groups contributing to dietary salt intake, estimated dietary sodium intake, visual analogical scale for salt intake, preference for salty/salted foods). A histological diagnosis was assigned based on the most severe lesion observed. H. pylori virulence was assessed by characterizing vacA and cagA genes. Odds ratios were estimated through age- and education-adjusted logistic regression models. The risk of IM was not significantly increased in H. pylori infected subjects with higher levels of salt consumption. The lack of association was consistent across measures of salt exposure, categories of H. pylori virulence, and types of IM. In conclusion, in this H. pylori positive population, salt intake did not increase the risk of any IM type, regardless of the virulence of the infecting strains.