Background <p>The probiotic may help restore treatment-impaired gut microbiota and promote beneficial bacterial colonization, but its specific impact on <i>Helicobacter pylori</i> (<i>H. pylori</i>) eradication efficacy and safety remains unclear. This study aimed to evaluate the role of <i>Bacillus subtilis</i> dual viable bacteria capsules (Medilac-S) as an adjunct to dual therapy, focusing on its impact on treatment safety and <i>H. pylori</i> eradication efficacy.</p> Methods <p>From April 1 to August 1, 2024, 220 <i>H. pylori</i>-positive patients were enrolled. They were randomly assigned to two treatment groups: the Probiotics Group (receiving Medilac-S, two capsules three times daily; vonoprazan 20&#xa0;mg twice daily; amoxicillin 1000&#xa0;mg three times daily) and the Dual Therapy Group (vonoprazan 20&#xa0;mg twice daily; amoxicillin 1000&#xa0;mg three times daily). Both groups underwent a 14-day treatment course. At least four weeks after treatment completion, a ¹³C-urea breath test was performed. <i>H. pylori</i> eradication rates, adverse event incidence, and medication compliance were compared between the two groups.</p> Results <p>Eradication rates did not differ significantly between groups in intention-to-treat (91.8% vs. 90.9%, <i>P</i> = 0.810), modified intention-to-treat (96.2% vs. 94.3%, <i>P</i> = 0.527), or per-protocol analyses (96.1% vs. 95.1%, <i>P</i> = 0.722). However, the Probiotics Group had significantly fewer adverse events (11.4% vs. 23.6%, <i>P</i> = 0.020). Medication compliance showed no significant difference between the groups (<i>P</i> = 0.414). The occurrence of adverse events was identified as a risk factor for eradication failure (OR = 12.000, <i>P</i> = 0.001).</p> Conclusion <p>Adding Medilac-S as an adjunct to vonoprazan-amoxicillin dual therapy resulted in satisfactory <i>H. pylori</i> eradication. Although the difference in eradication rates between the Probiotics Group and the Dual Therapy Group was not statistically significant, the Probiotics Group showed numerically higher, but not statistically significant, success rates across PP, mITT, and ITT analyses, along with a significant reduction in treatment-related adverse events. Patients experiencing adverse events were more likely to have eradication failure.</p> Trial registration <p><a href="https://www.medicalresearch.org.cn/">https://www.medicalresearch.org.cn/</a>, identifier ChiCTR2400082446. Registered on March 29, 2024.</p>