PurposeGiven the substantial risk of treatment failure in inflammatory bowel disease (IBD), adjuvant therapies may play a role in disease management. We aim to carry out a systematic review to examine the effects of structured exercise on the inflammatory response in patients with IBD. Our secondary aim is to examine the effect of structured exercise programmes on body composition given both an increase in visceral obesity and the presence of sarcopenia have deleterious effects on outcomes in IBD.MethodsA systematic review was carried out following the Methodological Expectations of Cochrane Intervention Reviews (MECIR) manual and the Cochrane Handbook for Systematic Reviews of Interventions. Title/Abstract and MeSH Terms were used to search for relevant studies.ResultsIn total, 1516 records were screened for eligibility, and 148 records were reviewed for eligibility, of which 16 were included and a further 7 studies were identified from hand searching references. Four studies included body composition outcomes, and 14 studies reviewed the inflammatory response to exercise.ConclusionFurther studies of adequate duration are required to include patients with more active disease to demonstrate an inflammatory response to exercise. Body composition measurements including muscle mass and visceral adiposity may play a key role in response to medical therapy in IBD and should be included as exploratory outcomes in future studies. A meta-analysis was not carried out due to the significant heterogeneity amongst studies.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00384-023-04437-2.