Background Affecting 40% of infants and young children worldwide, anaemia in sub-Saharan Africa hampers cognitive and physical development, often in ways that cannot be reversed. Iron-based micronutrient powders (MNPs) are recommended to combat anaemia, but concerns remain about their safety and effectiveness in malaria-endemic areas. We evaluated the impact of iron-based MNPs on growth measurements and malaria-related anaemia among preschool children in Ghana. Methods We conducted a secondary analysis of a cluster-randomized, double-blind, placebo-controlled trial in the Bono Region, Ghana. Children aged 6-35 months (n=1,958) received daily MNP containing 12{middle dot}5mg elemental iron or placebo for five months. Anthropometric indices, haemoglobin, and malaria parasitaemia were assessed at baseline and endline. Adjusted analysis of covariance (ANCOVA) models estimated effects on height-for-age (HAZ), weight-for-age (WAZ), and weight-for-height (WHZ) z scores. Binomial regression with identity link estimated risk differences for malaria-induced anaemia. Cluster-robust standard errors were applied at the compound level, and intracluster correlation coefficients (ICCs) were estimated. Results 1,815 (92{middle dot}7%) children completed the endline survey, but 1,806 were included in the final analysis. Baseline characteristics were balanced between groups. Iron-containing MNP had no significant effect on endline HAZ ({beta}=0{middle dot}026, p=0{middle dot}609), WAZ ({beta}=-0{middle dot}015, p=0{middle dot}719), or WHZ ({beta}=-0{middle dot}035, p=0{middle dot}463). However, the intervention reduced the risk of malaria-induced anaemia (risk difference 0{middle dot}050, 95% CI 0{middle dot}004-0{middle dot}096; p=0{middle dot}032). Female sex was associated with higher HAZ ({beta}=0{middle dot}149, p=0{middle dot}005). Conclusion Iron-containing MNP did not improve short-term growth but was associated with a modest reduction in malaria-induced anaemia. These findings support the safe use of iron fortification in malaria-endemic settings while underscoring the need for integrated strategies to address persistent growth faltering and gender specificity.