Malnutrition has remained a global public health issue, particularly in low- and middle-income countries (LMICs). Researchers have committed to studying malnutrition (especially in children under the age of five) to address the nine malnutrition targets, set by the WHO to be achieved by 2025. This study seeks to evaluate the prevalence, the individual and contextual predictors of malnutrition among children aged 6–59 months across Nigeria and its states. Two separates, independently collected, nationally representative cross-sectional surveys, the National Human Development Report (NHDR 2018) and the 2018 Nigeria Demographic and Health Survey (2018 NDHS) were linked for this study. Spatial map was used to describe the prevalence of malnutrition, a 3-level multivariate multilevel logistic regression models were fitted where children/individuals (at level 1) were nested in communities/clusters (at level 2) and nested in states (at level 3). A weighted sample of 7,770 children 6–59 months were considered in this study. The results showed that an estimated 43.6% of children aged 6–59 months are poorly nourished in Nigeria. The proportions of poorly nourished children were generally highest in the Northern Nigeria. Child’s gender, age, birth size, preceding birth order, anaemia status, maternal education, work status, body weight, household wealth status, number of bedrooms were among individual/household predictors of malnutrition. On the community level, being from community with high wealth index, distance to nearest health facilities is no big problem. Regional variations and gender inequality index were the state level predictors of malnutrition among children in Nigeria. This study has shown that two-third of children aged 6–59 months in Nigeria were poorly nourished, an indication of a growing concern of double burden of malnutrition in Nigeria.
