BackgroundMany patients with inflammatory bowel disease (IBD) use complementary and alternative medicine (CAM) for disease management. There is, however, a communication gap between patients and healthcare professionals regarding CAM use, where patients are hesitant to disclose CAM use to providers. The purpose of this study was to identify the quantity and assess the quality of CAM recommendations in IBD clinical practice guidelines (CPGs) using the Appraisal of Guidelines for Research and Evaluation II (AGREE II) instrument.MethodsMEDLINE, EMBASE, and CINAHL were systematically searched from 2011 to 2022 to find CPGs for the treatment and/or management of IBD. The Guidelines International Network (GIN) and National Center for Complementary and Integrative Health (NCCIH) websites were also searched. Eligible CPGs were assessed using the AGREE II instrument.ResultsNineteen CPGs made CAM recommendations for IBD and were included in this review. Average scaled domain percentages of CPGs were as follows (overall CPG, CAM section): scope and purpose (91.5%, 91.5%), clarity of presentation (90.3%, 64.0%), editorial independence (57.0%, 57.0%), stakeholder involvement (56.7%, 27.8%), rigour of development (54.7%, 45.9%), and applicability (14.6%, 2.1%).ConclusionsThe majority of CPGs with CAM recommendations were of low quality and their CAM sections scored substantially lower relative to other therapies in the overall CPG. In future updates, CPGs with low scaled-domain percentages could be improved in accordance with AGREE II and other guideline development resources. Further research investigating how CAM therapies can best be incorporated into IBD CPGs is warranted.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12906-023-04062-0.