Purpose: The surgical management of deep infiltrative endometriosis (DE) involving the rectum remains a challenge. The objective of this study was to assess the outcomes from a single tertiary center over a decade with an emphasis on the role of a protective loop ileostomy (PI). Methods: A retrospective review of outcomes for 168 patients managed between 2008 and 2018 is presented including 57 rectal shaves, 23 discoid excisions, and 88 segmental rectal resections. Results: The nodule size (mean±standard deviation) in the segmental resection group was 32.7±11.2 mm, 23.4±10.5 mm for discoid excision, and 18.8±6.0 mm for rectal shaves. A PI was performed in 19 elective cases (11.3%) usually for an ultra-low anastomosis <5 cm from the anal verge. All Clavien-Dindo grade III/IV complications occurred after segmental resections and included 5 anastomotic leaks, 6 rectovaginal fistulas, 2 ureteric fistulas, and 1 ureteric stenosis. Of 26 stomas (15.5%), there were 19 PIs, 3 secondary ileostomies (after complications), and 4 end colostomies. The median time to PI closure was 5.8 months (range, 0.4–16.7 months) in uncomplicated disease compared with 9.2 months (range, 4.7–18.4 months) when initial postoperative complications were recorded (P=0.019). Only 1 patient with a recurrent rectovaginal fistula had a permanent colostomy. Conclusion In patients with DE and rectal involvement a PI is selectively used for low anastomoses and complex pelvic reconstructions. Protective stomas and those used in the definitive management of a major postoperative complication can usually be reversed.