Purpose: To analyze rectal dose and changes in quality of life (QOL) measured with the Expanded Prostate and Cancer Index Composite (EPIC) bowel domain in patients being treated for prostate cancer with curative-intent proton beam therapy (PBT) within a large single-institution prospective registry. Materials and Methods: Data was collected from 243 patients with localized prostate cancer treated with PBT from 2016 to 2018. The EPIC survey was administered at baseline, end-of-treatment, 3, 6, and 12 months, then annually. Dose-volume histogram (DVH) parameters for the rectum were computed, and rectal dose was analyzed using BED (α/β = 3), EQD2Gy, and total dose. Repeated measures mixed models were implemented to determine the effect of patient, clinical, and treatment factors (including DVH) on patient-reported bowel symptom burden (EPIC-Bowel). Results: Treatment overall resulted in changes in EPIC-Bowel scores (baseline score = 93.7), most notably at end-of-treatment (90.6) and 12 months (89.7). However, they returned to baseline at 36 months (92.9). On multivariate modeling, rectal BED D25 (Gy) ≥23% was significantly associated with decline in QOL scores measuring bother (p < 0.01; 4.06 points different). Conclusion: Rectal doses, specifically BED D25 (Gy) ≥23%, are significantly associated with decline in bowel bother-related QOL in patients undergoing definitive radiotherapy for localized prostate cancer. This study demonstrates BED as an independent predictor of bowel QOL across dose fractionations of PBT.