Self-management programs that include cognitive behavioral strategies have been shown to improve gastrointestinal symptoms, psychological distress, and quality of life in persons with irritable bowel syndrome (IBS). However, less is known about the physiological impact of such a change. As part of a randomized controlled trial using a Comprehensive Self-Management (CSM) intervention (n = 126) compared to Usual Care (UC) (n = 62), cortisol levels were measured in four weekly first morning urine samples at baseline and at 3, 6, and 12 month follow-up. In addition, diary (28 days) ratings of stress were recorded at baseline, 3, 6, and 12 months. The omnibus test of all three outcome times showed no differences in urine cortisol levels between CSM and UC groups (p = .400); however, at 3 months the CSM group had significantly higher cortisol levels than the UC group (p = .012). The CSM group reported lower daily stress levels (p = .046 from omnibus test of all three time points) than UC, with the effect getting stronger over time. Despite marked improvements in reported stress and previously reported gastrointestinal and psychological distress symptoms at later follow-ups, the CSM program did not reduce urine cortisol levels in adults with IBS. These results suggest that the first void urine cortisol levels are not reflective of self reported daily stress in this patient population.