Managing the side effects of diarrhea, which is associated with intestinal microbial dysbiosis, is a crucial challenge in Helicobacter pylori eradication therapy. The aim of this study is to explore whether administration of a probiotic strain Enterococcus faecium 129 BIO 3B-R, a multi-antibiotic resistant lactic acid bacterium, influences the side effects of Helicobacter pylori eradication therapy in adults. Seventy-six adults undergoing this therapy were randomized to receive either Enterococcus faecium 129 BIO 3B-R or a placebo in a double-blind manner. No significant difference was observed in the incidence of diarrhea, the primary endpoint, or in any other secondary endpoints, including intestinal microbiota diversity, between two groups in the overall study population. However, in a post-hoc age-stratified analysis, participants aged 70 and older who used Enterococcus faecium 129 BIO 3B-R experienced tended to have more diarrhea during the eradication period but subsequently experienced significantly less diarrhea after eradication compared to the control group (23.1% vs. 60%). Treatment with Enterococcus faecium 129 BIO 3B-R also maintained higher α-diversity in their intestinal microbiota than those in the placebo group. Those data suggest that the administration of Enterococcus faecium 129 BIO 3B-R could potentially alleviate diarrhea and intestinal dysbiosis in over 70-year-old elderly patients undergoing Helicobacter pylori eradication.