Abstract Background and Aims Ustekinumab is approved for the treatment of Crohn’s disease CD. Systematically registered prospective real-world data are scarce. We therefore aimed to study the effectiveness, safety and usage of ustekinumab for CD in everyday practice. Methods We prospectively enrolled CD patients initiating ustekinumab in regular care between December 2016 and January 2019. Clinical (Harvey Bradshaw Index HBI), biochemical (C-reactive protein CRP and faecal calprotectin FCP), extra-intestinal manifestations and, peri-anal fistula activity, ustekinumab dosage, concomitant medication use, and adverse events were documented at weeks 0, 12, 24, and 52. The primary outcome was corticosteroid-free clinical remission. Results In total, 221 CD patients were included (98.6% anti-tumour necrosis factor TNF and 46.6% vedolizumab exposed) with a median follow-up of 52.0 weeks interquartile range 49.3–58.4. Corticosteroid-free clinical remission rates at weeks 24 and 52 were 38.2% and 37.1%, respectively. An initial dosing schedule of 8 weeks, compared to 12 weeks, correlated with a lower discontinuation rate 20.0% vs 42.6%, p = 0.01, but comparable corticosteroid-free clinical remission at week 52 (46.3% q8w vs 34.6% q12w, p = 0.20). There was no clinical benefit of combination therapy after 52 weeks when compared to ustekinumab monotherapy combi 40.6% vs mono 36.0%, p = 0.64. At baseline, 28 patients had active peri-anal fistula, of whom 35.7% showed complete clinical resolution after 24 weeks. During follow-up we encountered six severe infections 3.5 per 100 patient-years, with all patients being on concomitant immunosuppressant therapies. Ustekinumab treatment discontinuation was observed in 75 33.9% patients mainly due to lack of response. Conclusion Ustekinumab is a relatively safe and effective treatment option for CD patients with prior failure of anti-TNF and anti-integrin therapies.