To compare the distribution of malnutrition by socio-economic indicators (SEI) in Peruvian children under 5 years and women of reproductive age (WRA).We analysed data from the National Demographic and Family Health Survey. WHO criteria were used to define malnutrition indicators (overweight/obesity combined (OW); wasting/underweight; stunting/short stature; anaemia). Linear combination test was used to compare the prevalence of malnutrition by SEI (wealth index as a proxy of socio-economic status (SES); education; ethnicity). Prevalence ratio (PR) was used to describe disparities and associations between malnutrition and SEI.Peru (2015).Children (n 22 833) under 5 years and WRA (n 33 503; 5008 adolescents and 28 495 adults).The most prevalent form of malnutrition was anaemia (32·0 %) in children and OW in adolescent and adult WRA (31·3 and 65·1 %, respectively). Adjusted models showed that stunting and anaemia were significantly lower among children with high SES (PR = 0·25, 0·67), high-educated mothers (PR = 0·26, 0·76) and higher in indigenous children (PR = 1·3, 1·2); conversely, OW was higher among those with high SES and high-educated mothers (PR = 1·8, 1·6) compared with their lowest counterparts. In WRA, stunting/short stature was lower among those with high SES, high education and higher in indigenous adult women. OW in adolescents and adults was higher in high SES (PR = 1·4, 1·1), lower in indigenous adult women (PR = 0·84) and lower in high-educated adult women (PR = 0·86).In the studied population, the distribution of malnutrition was associated with SEI disparities. Effective policies that integrate actions to overcome the double burden of malnutrition and reduce disparities are needed.