Muscle-bone deficits are common in children with Crohn's disease (CD); however, few studies have assessed long-term musculoskeletal outcomes in adults with childhood onset CD. This study assessed the prevalence of musculoskeletal deficits in a cohort of young adults with childhood onset CD in comparison with healthy age and sex matched controls.This case-control study used 3-Tesla MRI and MRS to assess bone microarchitecture, cortical geometry and muscle area and adiposity at distal femur, and bone marrow adiposity of the lumbar spine, together with functional muscle tests and biochemical markers of the musclebone unit.Twenty-seven adults with CD with median (range) age 23.2 years (18.0, 36.1) and 27 controls with median age 22.9 years (18.2, 37.0) were recruited. Trabecular microarchitecture and cortical geometry of the distal femur and bone marrow adiposity of the lumbar spine were not different between CD and controls (p > 0.05 for all). Muscle cross sectional area was lower (p = 0.01) and muscle fat fraction was higher (p = 0.04) at the distal femur in CD compared to controls. CD participants had significantly lower grip strength (-4.3 kg [95% CI: -6.8, -1.8], p = 0.001) and lower limb muscle power relative to bodyweight (-5.0 W/kg [95% CI: -8.8, -1.2], p = 0.01). CD activity scores were negatively associated with trabecular bone volume (r = -0.40, p = 0.04) and muscle area (r = -0.41, p = 0.03).Young adults with well controlled CD managed with contemporary treatment strategies do not display abnormal bone microarchitecture or geometry at the distal femur but exhibit muscle deficits. The observed muscle deficits may predispose to musculoskeletal morbidity in future and interventions to improve muscle mass and function should be investigated.