The epidemiological and burden characteristics of nutritional deficiencies (ND) have been evolving, and it is crucial to identify geographical disparities and emerging trends. This study aimed to analyse the global, regional and national trends in the burden of ND over the past 30 years. Data were obtained from the Global Burden of Disease (GBD) 2019 database for the period 1990–2019. The study examined the incidence rates and disability-adjusted life years (DALY) of ND at various levels. Globally, the incidence rate of ND decreased from 2226·2 per 100 000 in 2019 to 2096·3 per 100 000 in the same year, indicating a decline of 5·8 %. The average annual percentage change (AAPC) was −0·21 (–0·31, −0·11). Similarly, DALY, prevalence and mortality rates of ND exhibited significant declines (AAPC = −3·21 (–3·45, −2·96), AAPC = −0·53 (–0·55, −0·51) and AAPC = −4·97 (–5·75, −4·19), respectively). The incidence rate of ND varied based on age group, sex, cause and geographical area. Moreover, a negative association was observed between incidence and the sociodemographic index. At the regional level, the South Asia and sub-Saharan Africa regions had the highest incidence rates of ND. In conclusion, the global incidence rate of ND showed a mixed pattern, while the DALY rate consistently declined. Additionally, prevalence and mortality rates of ND decreased between 1990 and 2019.