Background: Clinical Practice Guidelines (CPGs), serve as a framework for healthcare professionals to support therapeutic decisions and best practices for optimising patient care. However, if the guidelines do not sufficiently address all the important components of optimal care, their quality, validity, and impact are reduced. Despite multiple interventions, cases of malnutrition are still high due to the several factors linked to them. Therefore, there is a need to establish the methodological quality of malnutrition CPGs. Objective: To review and critically appraise the methodological quality of CPGs in managing malnutrition within the East African Community (EAC). Methods: We intend to focus on Integrated Management of Acute Malnutrition (IMAM) and Community Integrated Management of Malnutrition (CIMAM) guidelines. We will also focus on guidelines written in English or French and published in the last five years from the last search date or the latest guideline available. We will search the Ministry of Health websites of the EAC countries: Tanzania, Kenya, Uganda, South Sudan, Burundi, Rwanda, and the Democratic Republic of Congo. We will also search Health associations of the respective countries and their e-repositories. Using Google Search Engine, we will use the search terms "clinical practice guidelines, "nutrition guidelines", "nutrition protocols", "health guidelines"," "IMAM", "CIMAM" and "country". Five reviewers will independently select CPGs and extract data in English and French guidelines. We will conduct a quality assessment using the online version of the AGREE II tool across six domains and using the RIGHT reporting checklist. Descriptive statistics will be analysed using STATA software version 17 (Stata Corp LLC, College TX).