Objectives Abdominal complaints (AC) during exercise are a common problem in runners. Nutrition is known to play a role in exercise-related AC, but information on the role of habitual dietary intake is limited. We assessed the prevalence of AC in a large cohort of runners, and investigated its association with potential risk factors, with a particular focus on nutritional factors in the habitual diet. Methods A total of 1993 runners completed two online questionnaires: a general questionnaire on, among others, running habits and exercise-related AC and a Food Frequency Questionnaire. Runners with and without either upper AC (UAC) or lower AC (LAC) were compared regarding personal characteristics, running characteristics and habitual dietary intake. Results 1139 runners (57%) reported AC during and/or up to 3 hours after running: 302 runners (15%) reported UAC, 1115 (56%) LAC and 278 (14%) both. In about one-third of runners with AC, these complaints negatively affected their running. Exercise-related AC were positively associated with female gender, younger age and more intense running. Most associations with nutritional factors were observed only for LAC in men, with a higher intake of energy, all macronutrients and grain products in men with LAC. In both men and women, a higher intake of tea and unhealthy choices were associated with AC. Conclusion Exercise-related AC were quite prevalent, and in about one-third of the cases, AC impacted their running. Being female, having a younger age and running at higher intensity were positively associated with AC. Some aspects of the habitual diet were associated with AC. Most notable were positive associations for intake of fat, tea and unhealthy choices.