BACKGROUND: Exercise has been suggested to counteract specific complications of inflammatory bowel disease (IBD). However, its role as a therapeutic option remains poorly understood. Therefore, we conducted a systematic review and meta-analysis on the effects of exercise in IBD. METHODS: Five databases (MEDLINE, Embase, CINAHL, CENTRAL and SPORTDiscus) and three registers (Clinicaltrials.gov, WHO ICTRP and ISRCTN) were searched from inception to September 2022, for studies assessing the effects of structured exercise of at least 4 weeks duration on physiological and/or psychological outcomes in adults with IBD. Two independent reviewers screened records, assessed risk of bias using the Cochrane Risk of Bias (RoB 2.0) and ROBINS-I tools, and evaluated the certainty of evidence using the GRADE method. Data were meta-analysed using a random-effects model. RESULTS: From 4,123 citations, 15 studies (9 RCTs) were included, comprising of 637 participants (36% male). Pooled evidence from six RCTs indicated that exercise improved disease activity (SMD = -0.44; 95% CI [-0.82 to -0.07]; p = 0.02), but not disease-specific quality of life (QOL) (IBDQ total score; MD = 3.52; -2.00 to 9.04; p = 0.21) when compared to controls. Although meta-analysis could not be performed for other outcomes, benefits were identified in fatigue, muscular function, body composition, cardiorespiratory fitness, bone mineral density and psychological well-being. Fourteen exercise-related non-serious adverse events occurred. The overall certainty of evidence was low for disease activity and very low for HRQOL as a result of downgrading for risk of bias and imprecision. CONCLUSIONS: Structured exercise programmes improve disease activity, but not disease-specific QOL. Defining an optimal exercise prescription and synthesis of evidence in other outcomes, was limited by insufficient well-designed studies to ascertain the true effect of exercise training. This warrants further large-scale randomised trials employing standard exercise prescription to verify this effect to enable the implementation into clinical practice. REGISTRATION: This systematic review was prospectively registered in an international database of systematic reviews in health-related research (CRD42017077992; https://www.crd.york.ac.uk/prospero/).