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Background: Potassium‐competitive acid blockers (P‐CAB) are recommended for the treatment of Helicobacter pylori infections, but dual therapy of P‐CAB with amoxicillin has been poorly studied. The current study compared the efficacy, adverse reactions, compliance, and effects on gut microbiota of 14‐day vonoprazan‐amoxicillin (VA) dual therapy with esomeprazole, bismuth potassium citrate, amoxicillin, and metronidazole (EBAM) quadruple therapy in treatment‐naive patients with H. pylori. Materials and Methods: This was a multicenter, open‐label, randomized, and controlled, non‐inferiority study. Patients (n = 194) enrolled from six centers were randomly divided into either the VA or EBAM group. H. pylori eradication was determined using 13C urea breath tests (UBT) 4–6 weeks post‐treatment. Fecal samples were collected, and gut microbial populations were analyzed by 16S rDNA and metagenomic sequencing technology. Results: Eradication rates of H. pylori in the VA and EBAM groups were 88.7% and 91.8%, respectively, according to intention‐to‐treat (ITT) analysis; 95.6% and 96.7% with per‐protocol (PP) analysis; and 94.5% and 96.7% with modified ITT (mITT) analysis (all p > 0.05). The incidence of adverse reactions in the VA group was significantly lower compared to the EBAM group, and compliance within both groups was good. There was no difference in α‐diversity or microbial composition in the VA and EBAM groups at one‐month post‐treatment compared to baseline, except for a markedly reduced abundance of Bacteroides in the EBAM group. Conclusion: VA therapy achieved excellent eradication rates with low adverse reactions, good compliance, and little impact on gut microbiota. VA therapy should be recommended as a first‐line treatment against H. pylori. [ABSTRACT FROM AUTHOR]