Introduction The aim of this study was to investigate long‐term outcomes in terms of pain, quality of life (QoL), and gastrointestinal symptoms in women following colorectal surgery for deep endometriosis. Material and methods In this historical cohort, women who underwent surgical treatment for deep endometriosis by either nerve‐sparing full‐thickness discoid resection (DR) or colorectal segmental resection (SR) between March 2011 and August 2016 were re‐evaluated through telephone interviews about their long‐term pain symptoms, subjective overall QoL as rated using a score from 0 (worst) to 10 (optimal), and gastrointestinal outcomes reflected by lower anterior resection syndrome (LARS) following a first postsurgical evaluation (visit 1) published previously and a long‐term follow‐up evaluation (visit 2). Results The median long‐term follow‐up time was 35.4 months at visit 1 and 86 months at visit 2. Of 134 patients, 77 were eligible for final analysis and 57 were lost to follow‐up. Compared with presurgical values, QoL scores were significantly increased at both postsurgical evaluation visits in both the SR cohort (scores of 3, 8.5, and 10 at the presurgical visit, visit 1, and visit 2, respectively; p < 0.001) and the DR cohort (scores of 3, 9, and 10, respectively; p < 0.001). Pain scores for dysmenorrhea (SR group scores of 8, 2, and 2, respectively; p < 0.001; DR group scores of 9, 2, and 1, respectively; p < 0.001), dyspareunia (SR group scores of 4, 0, and 0, respectively; p < 0.001; DR group scores of 5, 0, and 1, respectively; p = 0.003), and dyschezia (SR group scores of 8, 2, and 2, respectively; p < 0.001; DR group scores of 9, 2, and 1, respectively; p < 0.001) significantly decreased after surgery and remained stable in both cohorts over the follow‐up period. Minor and major LARS, reflecting gastrointestinal function, was observed in 6.5% and 8.1% of the SR group and in 13.3% and 6.7% of the DR group, respectively, at visit 1 and in 3.2% and 3.2% of the SR group and 0% and 0% of the DR group, respectively, at visit 2, without significant differences between the SR and DR groups. Conclusions Colorectal surgery for deep endometriosis, either by DR or SR, provides stable and long‐term pain relief with low rates of permanent gastrointestinal function impairment.