Introduction: One of the topics that show differences of opinion in the scientific field of nutrition is the recommendation by clinical practice guidelines (CPGs) of an immunomodulatory diet with arginine, nucleotides and omega-3 for individuals diagnosed with cancer undergoing major surgery. The quality of the recommendations is directly related to credibility, transparency and rigour in their development, but also to the quality of the studies published and available for inclusion in the recommendation, such as systematic reviews (SRs) and randomised clinical trials. The aim of this study is to evaluate the methodological quality of the recommendation of perioperative immunomodulatory supplementation for individuals with gastrointestinal and head and neck cancer, the CPGs, and the studies that support the recommendations. Methods and analysis: We will conduct a systematic search for CPGs. Recommendations for nutritional supplementation with immunomodulatory substrates for individuals undergoing major oncological surgery will be analysed using the Appraisal of Guidelines Research and Evaluation-Recommendations Excellence tool. CPGs will be analysed using the Appraisal of Guidelines Research and Evaluation II tool. The SRs cited in the recommendations will be analysed using the A Measurement Tool to Assess Systematic Reviews II tool and additional questions regarding heterogeneity in reviews. The clinical trials cited in the SRs and in the guideline recommendations (when applicable) will be analysed according to questions regarding heterogeneity in trials. The results will be presented in tables or charts using descriptive analyses. Ethics and dissemination: The results of this study will be disseminated through relevant conferences and peer-reviewed journals. Protocol registration number: 10.17605/OSF.IO/X2GYT.