There is an ongoing debate on surgical techniques for colorectal deep endometriosis (DE) and their effects on gastrointestinal (GI) function. The aim of this study was to prospectively investigate the differences in pre- and postsurgical GI function, health profiles and pain symptoms in women undergoing colorectal surgery for symptomatic DE either with a modified segmental resection technique, so-called nerve-vessel sparing segmental resection (NVSSR), or full thickness discoid resection (FTDR). Complication rates and fertility outcomes were also evaluated. A total of 162 consecutive patients, 125 (77.2%) of whom underwent NVSSR and 37 (22.8%) FTDR, were evaluated regarding complication rates. Furthermore a lower anterior resection syndrome (LARS) scores, gastrointestinal function-related quality of life index(GIQLI), pain symptoms, endometriosis health profile (EHP-30) parameters were analyzed pre- and post-surgery in a final cohort of 121 patients. There was no difference between postsurgical prevalence of LARS in either surgery group (14/98, 14.1% NVSSR; 2/23, 8.6% FTDR), with significantly decreased LARS scores and increased GIQLI values before vs after surgery in both groups (P < 0.001). The overall grade III complication rate was 7/162 (4.3%) with no significant differences between NVSSR and FTDR groups. Overall, EHP-30 and pain scores significantly decreased after a median follow-up of 41 (± 17.6) months (EHP-30 51.1, SD 21.5 vs 12.7, SD 19.3, P < 0.001; dysmenorrhea, dyspareunia, dyschezia all P < 0.001 both cohorts, respectively). The overall life birth rate and postsurgical pregnancy in infertile patients undergoing NVSSR and FTDR was respectively 58.1% in 25/43 patients; 55.6% in 5/9 patients; 56.0% in 14/25 patients and 100% in 5/5 patients. NVSSR and FTDR for symptomatic colorectal DE confer a significant amelioration of GI function reflected by decreased LARS symptoms and increased GIQLI scores with no differences in postsurgical function in between the two techniques. Both techniques confer similar complication rates and effects on pain reduction and health profiles.