Micronutrients powder (MNP) can prevent anaemia amongst children 6–23 months old. However, evidence of an effect on growth is limited and concerns about the safety of iron‐containing MNP interventions limits their applicability. In a cluster randomized controlled intervention, we evaluated the effectiveness of a nutritional package including counselling and provision of MNP to improve the nutritional status of children aged 6–23 months and the effect of sustained use of MNP on morbidity in a malaria‐endemic area. Child feeding practises and nutritional status were assessed through cross‐sectional surveys. Biweekly morbidity surveillance and anthropometry measurements were carried out in a nested cohort study. No significant differences in the prevalence of wasting (−0.7% [−6.8, 5.3] points; p = .805), stunting (+4.6% [−2.9, 12.0] points; p = .201), or mean length‐for‐age z‐score and weight‐for‐length z‐score scores were found between study groups. The proportion of children with a minimum dietary diversity score and those with a minimum acceptable diet significantly increased in the intervention group compared with the control by 6.5% points (p = .043) and 5.8% points (p = .037), respectively. There were no significant differences in the risk of diarrhoea (RR: 1.68, 95% CI [0.94, 3.08]), fever (RR: 1.20 [0.82, 1.77]), and malaria (RR: 0.68 [0.37, 1.26]) between study groups. In the nested study, the rate of linear growth was higher in the intervention than in the control group by 0.013 SD/month (p = .027). In a programmatic intervention, MNP and nutrition education marginally improved child feeding practises and growth, without increasing morbidity from malaria or fever.