Although inflammatory bowel disease (IBD) is known to be associated with lower psychological health, research regarding which specific symptoms may lead to psychological dysfunction in IBD patients is inexistent. Further, the role played by emotion regulation, including the maladaptive process of cognitive fusion, in IBD patients’ psychological functioning is also scarcely explored in this population. The present study aimed at filling these research gaps. Two hundred and sixteen patients diagnosed with IBD filled self-report instruments on an online platform in three times. These waves of assessment occurred at baseline, and 9 and 18 months later. Results revealed that of the 10 measured IBD symptoms, only fatigue, bloody stools and abdominal distension at baseline were negatively associated patients’ level of psychological health at Wave 3. Nevertheless, a hierarchical regression analysis demonstrated that none of these symptoms were significant predictors of psychological health measured 18 months later. When cognitive fusion at baseline was added to the model, it became the only significant predictor of psychological health at Wave 3, with an effect of −0.34 (P < 0.001). These findings suggest that it is not the experience of physical symptomatology that directly leads to lower psychological health in IBD patients, but rather the way patients deal with adverse internal experiences, i.e., the type of emotion regulation involved. This study reveals cognitive fusion as a harmful process for the determination of IBD patients’ psychological functioning. Future studies should thus explore the meditational effect of cognitive fusion in the association between IBD symptomatology and decreased psychological health.