Introduction: Stunting among children under the age of five is a major public health challenge in Indonesia. Several factors have been identified as influencing stunting; however, Indonesia has several islands with unique characteristics that may impact them. Objectives: This study aims to investigate factors associated with district-level stunting prevalence while accounting for island-level variation. Methods: This study utilised data mainly from the 2020 Food Security and Vulnerability Atlas (FSVA) of the Indonesian Ministry of Agriculture. The FSVA collected 2019 indicators and was published in 2020. The independent variables are classified into two levels: the district level (514 districts) and the island level (eight major islands). The analysis was done using multilevel linear regression. Results: Most districts (473 out of 514) have a high or very high prevalence of stunting. The results showed that poverty, households with food expenditures greater than 65%, households without water, and women’s education were all positively associated with stunting at the district level, but health personnel coverage was negatively associated. At the island level, Gross Regional Domestic Products (GRDP) were found to be negatively linked with stunting. Conclusion: Poverty and lack of basic infrastructure continue to be major contributors to stunting. Given Indonesia’s breadth and number of islands, stunting-reduction initiatives are customised to regional challenges, with a focus on regions where stunting is more prevalent. © 2025 Sociedad espanola de dietetica. All rights reserved.