Low- and middle-income countries (LMICs) suffered the most from nutritional deficiencies (NDs). Although decades of efforts have reduced it, little is known about the changing trajectory of ND burden in LMICs. By extracting data of the Global Burden of Diseases, Injuries, and Risk Factors Study 2019, we calculated indicators of incidence and disability-adjusted life years (DALYs) to measure the burden of NDs and its main subcategories in LMICs, including protein-energy malnutrition, iodine deficiency, vitamin A deficiency, dietary iron deficiency, and other nutritional deficiencies by sex, age and spatial patterns. In LMICs, ND incidence still increased in the age group 15+ born before 2005, especially in males. The effort of reducing the DALYs of NDs has generated a strong decline in per age group. In the main subcategories of NDs, protein-energy malnutrition incidence in males age 45+ born before 1970 still increased. Despite vitamin A deficiency incidence and dietary iron deficiency, DALYs strongly experienced decreases over three decades while still remaining at the heaviest level in 2019, especially in females and children under 5 years. The top largest tendency estimates occurred in Mali’ females and Bhutan’ males. Zimbabwe was the only country with increased DALYs rate tendency in both sexes.