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Methods From April 2023 to October 2024, gastric muscularis propria tumours\u2009\u2264\u200910\u00a0mm in size that were resected via ESR-EB or ESE were prospectively collected at Shenzhen Second People\u2019s Hospital. The general clinical characteristics, tumour location, tumour size, growth pattern, histological diagnosis, operation time, resection time, complete resection rate, incidence of intraoperative complications, postoperative antibiotic usage rate, postoperative hospital stay, follow-up time, and presence of recurrence and metastasis were compared between the two groups. Results A total of 245 patients were enrolled, 14 of whom were excluded due to having multiple muscularis propria tumours in the stomach. Therefore, 231 patients were ultimately included for analysis (108 patients in the ESR-EB group and 123 patients in the ESE group). There were no differences in sex or tumour growth pattern, but there were significant differences in age, tumour size and tumour location (P\u2009&lt;\u20090.05). Propensity score matching (PSM) was used, resulting in 54 patients in each group. The operation time was significantly shorter in the ESR-EB group than in the ESE group (21.61\u2009\u00b1\u20099.31\u00a0min vs. 33.15\u2009\u00b1\u200919.00\u00a0min; P\u2009&lt;\u20090.001). The resection time significantly shorter in the ESE-EB group than in the ESE group (9.85\u2009\u00b1\u20096.09\u00a0min vs. 26.39\u2009\u00b1\u200918.16\u00a0min; P\u2009&lt;\u20090.001). A 100% complete resection rate was achieved in both groups. There was no significant difference in postoperative hospital stay between the two groups (5.81\u2009\u00b1\u20091.41 d vs. 5.39\u2009\u00b1\u20091.53 d; P\u2009=\u20090.161). GISTs represented the most common histological diagnosis in both groups. Thirty-two patients (59.26%) in the ESR-EB group had gastrointestinal stromal tumours (GISTs), and 27 patients (50.00%) in the ESE group had GISTs. The second most common histological diagnosis was leiomyoma, and schwannoma was the rarest histological diagnosis. There was no significant difference between the two groups in terms of histological diagnoses (P\u2009=\u20090.463). Perforation was the most common intraoperative complication, affecting 30 patients (55.56%) in the ESR-EB group and 21 patients (38.89%) in the ESE group; this difference was not significant (P\u2009=\u20090.083). Five patients (9.26%) in the ESR-EB group experienced intraoperative bleeding, which was significantly lower than the 18 patients (33.33%) in the ESE group (P\u2009=\u20090.002). All perforations and bleeding were successfully managed endoscopically. Twenty-six (48.15%) patients in the ESR-EB group and 17 (31.48%) patients in the ESE group used postoperative antibiotics; this difference was not significant (P\u2009=\u20090.077). There was no significant difference in follow-up time between the ESR-EB and ESE groups (240.50\u2009\u00b1\u200957.14 d vs. 238.41\u2009\u00b1\u200957.48 d; P\u2009=\u20090.054). Neither group experienced recurrence or metastasis during the follow-up period. Conclusion Both ESR-EB and ESE are effective and safe methods for the resection of gastric muscularis propria tumours. However, ESR-EB has a low incidence of intraoperative bleeding as well as short operation and resection times; thus, ESR-EB is a safer and time-saving endoscopic technique. 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