Anemia adversely affects children’s cognitive and motor development and remains a global public health problem. This study aimed to identify the individual, feeding, household, and community determinants of anemia among children in Mozambique. We used pooled datasets of two Mozambique representative population-based surveys: the 2011 and 2022–2023 Demographic and Health Surveys. A total sample of 8143 children aged 6–59 months with available hemoglobin testing was included. Multilevel mixed-effects analysis was performed using STATA (18.0). Over a decade, the prevalence of anemia in children aged 6–59 months remained high, increasing slightly from 69.1% in 2011 to 72.9% in 2022. Children aged 6–11 months were more likely to have anemia than those in other age groups. Children who suffered from illnesses (aOR = 1.44, 95% CI = 1.18–1.75), lived in female-headed households (aOR = 1.16, 95% CI = 1.01–1.32), and who lived in households with unimproved drinking water sources (aOR = 1.40, 95% CI = 1.19–1.65) were more likely to have anemia than their peers. Overall, 16% of the variability in anemia prevalence was attributed to differences between clusters (ICC = 0.16). Childhood anemia remains a critical public health challenge in Mozambique, with prevalence rates exceeding the average for sub-Saharan Africa. Multisectoral approaches to improve the provision of essential supplies and the monitoring of primary healthcare for at-risk children, increased investments in rural development and sustainable agriculture, water sanitation, social care, and gender-sensitive work policies can help address childhood anemia.