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Data suggest dietary modification can improve clinical responses in inflammatory bowel disease (IBD). The goal of this study was to determine the efficacy of an autoimmune protocol diet in patients with Crohn's disease and ulcerative colitis.We enrolled adults with active IBD (Harvey–Bradshaw index ≥ 5 or partial Mayo score ≥3 and erosions on endoscopy and/or elevated fecal calprotectin). For the autoimmune protocol, patients underwent 6-week elimination followed by 5-week maintenance phase. Clinical indices, laboratories, and biomarkers were assessed at baseline and weeks 6 and 11. Endoscopy was performed at study completion.The final cohort included 15 patients with IBD, with mean disease duration 19 years (SD 14.6) and active biological use in 7 (47%) patients. Nutrient repletion was initiated for deficiencies in vitamin D (n = 3) and iron (n = 6). From week 0 to weeks 6 and 11, mean partial Mayo score significantly improved from 5.8 (SD 1.2) to 1.2 (SD 2.0) and 1.0 (SD 2.0) for ulcerative colitis, and mean Harvey–Bradshaw index significantly improved from 7 (SD 1.5) to 3.6 (SD 2.1) and 3.4 (SD 2.6) for Crohn's disease. C-reactive protein did not significantly change during study. Mean fecal calprotectin improved from 471 (SD 562) to 112 (SD 104) at week 11 (P = 0.12). Among those with follow-up endoscopy at week 11 (n = 7), improvements were noted in simple endoscopic score for Crohn's disease (n = 1), Rutgeerts score (n = 1), and Mayo endoscopy subscore (n = 4).Dietary elimination can improve symptoms and endoscopic inflammation in patients with IBD. Randomized controlled trials are warranted.