Purpose: Surgical technique in bariatric surgery has been refined over the past decades. This study analysed the effect of changing the stapling protocol on the quality of life (QoL) at a midterm follow-up. Methods: The retrospective cohort study included patients undergoing Roux-en-Y gastric bypass between June 2012 and March 2016. Patients were stratified into the circular stapling protocol (CSP, n = 117) or the linear stapling protocol (LSP, n = 118). QoL was quantified by the Moorehead score at 12, 24 and 60 months. Multivariate testing was used to identify confounders. Results: The age was 42.8 ± 11.5 years and the body mass index (BMI) was 43.8 ± 6.2 kg/m2, with no baseline intergroup differences. Overall baseline Moorehead score was 0.42 ± 1.1 and improved in both groups after 12 months (1.97 ± 0.74, p < 0.001), 24 months (1.86 ± 0.79, p < 0.001) and 60 months (1.71 ± 0.9, p < 0.001). LSP was associated with improved Moorehead score after 60 months (odds ratio [OR] 1.251, 95% confidence interval [CI] 1.06–1.48, p = 0.010). Overall, a drop of mean BMI occurred and this effect lasted throughout the observation period (− 12.48 kg/m2, p < 0.001). More profound BMI reduction was further positively associated with Moorehead scores after 24 and after 60 months (OR 0.97, p = 0.028; OR 0.96, p = 0.007). Complications, rehospitalisations and reoperations were more frequent in the CSP group (50% vs 23.7%, p < 0.001; 39.7% vs 22.9%, p = 0.009; 37.1% vs 18.6%, p = 0.003). Conclusion: The CSP and LSP achieve a long-lasting increase in QoL, although the LSP is associated with fewer complications, persistent weight loss and improved Moorehead score. Therefore, the LSP might be considered the favourable protocol in Roux-en-Y gastric bypass. [ABSTRACT FROM AUTHOR]