Background The randomized controlled PROPP trial (DKRS00004191) showed that pylorus-resecting pancreatoduodenectomy (PR) is not superior to the pylorus-preserving procedure (PP) in terms of perioperative outcome, specifically in reduction of delayed gastric emptying. Non-superiority of PR was also confirmed in a recent meta-analysis of randomized controlled trials. However, long-term data on morbidity and quality of life after PP compared to PR are sparse. The aim of this study was to investigate long-term outcomes of patients included in the PROPP trial. Methods Between February 2013 and June 2016, a total of 188 patients underwent PD and were intraoperatively randomized to either preservation or resection of the pylorus (95 vs. 93 patients). For long-term follow-up, morbidity and quality of life (EORTC QLQ-C30/PAN26) were monitored until January 1, 2018. Statistical analysis was performed on an intention-to-treat basis. Results The mean duration of follow-up was 34.3 (± 11.3) months. Sixty-three of the 188 patients had died (PP n  = 33, PR n  = 30), 29 patients were lost to follow-up (PP n  = 17, PR n  = 12), and the remaining 96 patients were included in long-term follow-up (PP n  = 45, PR n  = 51). There was no difference between PP and PR patients regarding endocrine and exocrine pancreatic function, receipt of adjuvant/palliative chemotherapy, cancer recurrence, and other relevant characteristics. Late cholangitis occurred significantly more often in patients following pylorus resection ( P  = 0.042). Reoperations, readmissions to hospital, and quality of life scores except pain were comparable between the two study groups. Conclusions Similar to short-term results, long-term follow-up showed no significant differences between pylorus resection compared to pylorus preservation.