Abstract Background According to the WHO, malnutrition refers to deficiency, excess, or imbalance in a person’s intake of energy and/or nutrients. Children under five are especially vulnerable to malnutrition. The problem is widespread, but it is particularly prevalent in West African countries, where a prevalence of 30% stunting, 6.7% wasting and 2.4% overweight was described in 2022. In this study, we aimed to evaluate malnutrition in Guinea-Bissau (GB), a low-income country in West Africa. Methods We conducted a cross-sectional study between May and June 2023 on a representative sample of 1608 children aged 6 to 59 months, who had access to health care in all 11 regions of GB. Nutritional status was assessed by evaluating weight for height/length, weight for age, height/length for age, and hemoglobin concentration was determined using a portable hemoglobin analyzer. Furthermore, semi-structured questionnaires were applied to children’s parents, including questions on sociodemographic and behavioral factors, such as ethnicity, parental literacy, health care, and dietary patterns. Results 802 boys and 806 girls were included in the study, with a mean age of 26 months. Malnutrition rates were comparable to those described in other West African countries. We found wasting rates of 8,3%, stunting rates of 24,3%, low weight rates of 17,4%, and overweight rates of 2,4% among children under five. Importantly, 55.9% of the children had anemia: 23.6% had mild anemia, 31.1% had moderate anemia, and 1.2% had severe anemia. Statistical analyses are underway to investigate factors associated with malnutrition. Conclusions An important challenge in global health is combating malnutrition in all its forms. The identified prevalence of malnutrition in GB is high and emphasizes the importance of developing strategies and policies with local authorities so that the Sustainable Development Goals and Global Goals of Nutrition can be achieved and health outcomes improved. Key messages • Collaboration essential: researchers, policymakers, healthcare, and local authorities must unite for targeted malnutrition interventions. • Sustainable development in GB hinges on addressing malnutrition among its children through concerted efforts.