Objectives: Treatment of patients with inflammatory bowel disease (IBD) should aim at achieving mucosal healing. However, monitoring schedules to support this goal remain undefined. We aimed to identify patients’ and physicians’ preferences regarding monitoring strategy and investigated the feasibility of such a strategy. Methods: Elements considered relevant for monitoring were identified in questionnaire surveys among 1) patients with IBD receiving biologic agents (n = 172) and 2) their physicians (n = 87). Adherence to a monitoring strategy incorporating these elements was investigated in a retrospective cohort of patients with IBD treated with biologic agents (n = 139). Results: Patients considered blood and stool samples, endoscopies, and magnetic resonance imaging (MRI) to be relevant aspects of monitoring their disease. However, patients also considered stool samples and endoscopies unpleasant. Physicians considered blood samples (99%), medical consultations (99%), fecal calprotectin (85%), endoscopy (78%), and MRI (71%) to be important aspects of IBD monitoring but considered endoscopies and MRI relevant only at clinical signs of relapse. A review of the clinical use of monitoring strategies including the elements identified above revealed high adherence for blood samples and disease activity indices (92%), but low adherence for fecal calprotectin (38%), therapeutic drug monitoring (38%), and endoscopies (32%). Conclusion: Important tools for evaluating mucosal healing (e.g., endoscopy) were rated highly unpleasant by patients, and physicians found endoscopies/MRI relevant only in case of relapse. These findings were reflected by low rates of adherence to use of these monitoring tools. In defining monitoring schedules to help achieve treatment goals, these important barriers must be addressed.