Background Vietnam is facing a double burden of malnutrition, with increasing prevalence of overweight coexisting with undernutrition (stunting, and thinness) and micronutrient deficiencies (MNDs). Although malnutrition during female adolescence leads to poor health outcomes and may have intergenerational effects on offspring, no studies have investigated MNDs and nutritional status among contemporary Vietnamese female adolescents. Methods Data from 10- to 18-year-old female adolescents (n=1,471) in the nationally-representative Vietnam General Nutrition Survey 2020 were analysed. Blood nutritional biomarkers, anthropometric measurements, and socio-demographic data were collected and the association between nutrition status and MNDs were analysed; with anaemia, iron deficiency (ID), iron deficiency anaemia, low serum zinc, low serum retinol, and any MNDs as specified outcomes. Findings Prevalence of overweight, stunting, and thinness was 27.2%, 14.3%, and 6.9%, respectively. Low serum zinc was common (39.8%), as was ID (9.8%). Bivariate analyses showed that older age (16-18 years old), ethnic minority, lower wealth index, and inflammation were associated with MNDs. In the adjusted logistic regressions, stunting was associated with an increased odds ratio (AOR) and [95% confidence intervals] of low serum retinol (8.92 [2.26, 35.15], p<0.01), as did thinness (12.25 [3.47, 43.33], p<0.01). Stunting was also associated with an increased odd of having any one MND (1.88 [1.13, 3.12], p<0.05). Interpretation More female adolescents were overweight than undernourished in Vietnam in 2020. However, undernutrition, low serum zinc, and ID remain prevalent. Food systems approaches should be considered to stem the stark increase in the double burden of malnutrition in young people living in Vietnam. Funding UK BBSRC BB/T008989/1.