<b><i>Introduction:</i></b> Stress and lifestyle factors impact the course of Crohn’s disease (CD). Our primary objective was to assess whether patients with CD benefit from a mind-body-medicine stress management and lifestyle modification (MBM) program. <b><i>Methods:</i></b> This 9-month two-arm pilot trial was conducted in Bamberg, Germany (2020–2021). Patients (18–75 years) with mild to moderate activity of CD and stable medication were enrolled and randomly assigned to either a 10-week MBM program (intervention group, IG) or a single 90-min education session (waiting list control group, CG). Primary endpoints were quality of life (IBDQ) and disease activity (HBI). Secondary endpoints were emotional distress, core self-evaluation, and inflammatory biomarkers 3 and 9 months after baseline assessment. <b><i>Results:</i></b> We analyzed data from 37 patients (IG: <i>n</i> = 19, mean ± SD age 49.6 ± 13.1 years, 68% female; CG: 18, 46.8 ± 11.4, 67% female). Immediately after the intervention, 79% (IG) and 44% (CG) experienced a clinically relevant improvement (IBDQ score ≥16 points). This was similar after 9 months (63% vs. 44%). There was no difference in disease activity (3 months: <i>p</i> = 0.082, 95% CI −1.3 to 2.6; 9 months: <i>p</i> = 0.251, 95% CI −1.2 to 2.5). Secondary outcomes indicated improvements in emotional distress, core self-evaluation, erythrocyte sedimentation rate after three and in emotional distress, T-cell profiling in the blood, and fecal lactoferrin and calprotectin group after 9 months in the IG. <b><i>Conclusion:</i></b> Our study suggested benefits of a multimodal stress management and lifestyle modification program for patients with CD. Larger trials are needed to determine if the program can supplement or at least partially replace pharmacological treatment approaches.