Background Since Inoue performed the first POEM in 2008, safety and efficacy have been well-established. Early studies focused on refining the technique and avoiding incomplete myotomy. Following the discovery that many patients with abnormal acid exposure are asymptomatic, the focus shifted to post-POEM reflux, but no studies have identified any associated procedural factors. In this study, we examined the intermediate-term results of our previous randomized controlled trial, with particular attention to post-POEM reflux. Methods Previously, 100 consecutive patients were randomized to either double- or single-scope POEM. Endoscopy was conducted 2 months post-POEM and annually thereafter. Patients were included in the present study if they completed endoscopy ≥ 6 months post-POEM, and the clinical results of both groups were analyzed with particular attention to clinical efficacy and post-POEM reflux. Results Median follow-up was 3 years, and most myotomies were performed in the posterior location. The final gastric myotomy length was longer in the double-scope group (3.3 vs. 2.6 cm). Clinical efficacy (≥ 80%) and rates of post-POEM reflux (~ 60%) were similar; however, there was a higher incidence of moderate esophagitis (Los Angeles Grade B) in the double-scope group (25% vs. 4%). There were no cases of severe esophagitis (Los Angeles Grade C/D). Among patients with normal endoscopy at 2 months, > 40% developed erosive esophagitis on intermediate-term follow-up. Conclusions This is the first study to demonstrate a procedural factor that increases post-POEM esophagitis. Gastric myotomy > 2.5 cm results in increased rates of moderate esophagitis without improving clinical efficacy. Some patients developed esophagitis in a delayed fashion, emphasizing the importance of ongoing surveillance. We also believe that preserving the gastric sling fibers may help to reduce reflux rates. The double-scope method may help to control myotomy length (2.0–2.5 cm) and direction (lesser curve to avoid the gastric sling) to help maximize clinical efficacy while minimizing post-POEM reflux.