Abstract Background The effectiveness of biologics for improving long-term outcomes in patients with Crohn’s disease [CD] is still controversial. In this nationwide study, we aimed to evaluate trends of long-term outcomes in all CD patients in Israel during the biologics era. Methods Trends of outcomes were analysed using data from the four Israeli health maintenance organisations, covering 98% of the population; joinpoint regression models were used to explore changes of these trends over 2005 to 2019. Results A total of 16 936 patients were diagnosed with CD in Israel since 2005 (2932 [17%] paediatric onset, 14 004 [83%] adult onset) with 114 947 person-years of follow-up. The cumulative rate of any CD related surgery was 5%, 9%, 11%, and 14% at 1, 3, 5, and 10 years from diagnosis. The increase in use of biologics was sharp (from 8.9% to 36%; average annual percent change [AAPC], 14.3%), and the time to biologics was shorter in recent years (median time of 4.8 [1.9–8.1] years in those diagnosed in 2005–2008 compared with 0.5 [0.2–1.1] years in those diagnosed in 2015–2018; p < 0.001). A significant decrease was noted in the hazard of hospitalisations (1.3 [0.1–4.6] years compared with 0.2 [0.02–0.9] years; p < 0.001), steroid dependency (1.5 [0.2–5.4] years compared with 0.1 [0.02–0.4] years; p < 0.001), and intestinal surgeries [4.7 [1.6–8.2] years compared with 0.6 [0.2–1.4] years; p < 0.001), but not of perianal surgery (4.2 [1.1–7.7] years compared with 0.6 [0.2–1.4] years; p = 0.2). Outcomes were consistently worse in paediatric onset compared with adults. Conclusions The rates of hospitalisations, steroid dependency, and intestinal resections decreased in association with increased use of biologics both in children and in adults, but not the rate of perianal surgeries.