Abstract Background Inflammatory bowel diseases (IBDs) are diseases of the immune system that share some genetic and lifestyle-related predisposing factors. Increasing incidences have been reported in all age groups. Based on experimental studies suggesting a role of physical activity on intestinal inflammation, this study aimed to investigate the association between leisure time physical activity and the risk of IBD in older adults. Methods The study is a prospective cohort study using Danish registry data and questionnaire data from the Danish “Diet, Cancer and Health” cohort. The outcome IBD was defined as having at least two main diagnoses of Crohn’s disease or ulcerative colitis registered in the National Patient Registry from the period between December 1993 and May 1997 with an average follow-up of 25 years. Cox proportional hazard models were used to estimate hazard-ratios for IBD onset associated with being physically active and with levels of the metabolic equivalent of task (MET) hours/week of physical activity and hours/week spent on six types of physical activity. All analyses were adjusted for potential confounders. Furthermore, the analyses were stratified according to age-group, occupational physical activity, smoking, BMI and work status to test for effect modification. Results In total, 54,645 men and women aged between 50 and 64 years were included, and of which there were 529 cases. When comparing physically active with inactive participants measured by MET hours/week there was no statistically significant difference in risk of IBD (0.89 [0.13; 6.27]), regardless of how participation was measured. Results did not indicate any dose-response effect when comparing quartile groups of MET hours/week (HR = 0.97 [0.76; 1.22], HR = 0.82 [0.64; 1.05] and HR = 0.83 [0.65; 1.07] or whether five of the six types of activities were compared with the lowest quartile as reference. For do-it-yourself-work, the third quartile of hours/week was associated with a higher risk of IBD compared to the second quartile of hours/week (HR = 1.44 [1.10; 1.90]. No effect modification was found. Conclusions There was no association between physical activity and risk of IBD when comparing physically active with inactive participants. Neither did the results indicate any dose-response effect when comparing quartile groups of MET hours/week with the lowest quartile as reference. Do-it-yourself work, however, appeared to be associated with a higher risk of IBD when comparing the third quartile with the second quartile of hours/week. The study has clinical relevance by its contribution to the explanatory field of the causes of IBD. However, the study has some limitations, and further research is needed to clarify associations between physical activity and risk of IBD.