BackgroundMalaria remains a burden globally, with the African region accounting for 94% of the overall disease burden and deaths in 2019. It is the major cause of morbidity and mortality among children in Nigeria. Though different environmental factors have been assessed to influence the distribution and transmission of malaria vectors, there is a shortage of information on how they may influence malaria transmission among under-fives in Nigeria.MethodsThis study was based on the secondary data analysis of the Nigeria Malaria Indicator Survey 2021. The study sample comprised 10,645 women (aged 15–49) who delivered a child in the 2 years preceding the survey. The study was restricted to under-fives. Logistic regression was used to identify factors associated with the risk of malaria.ResultsThere was a positive association between the risk of malaria and heard/seen malaria messages in the last 6 months (AOR 1.39, 95% CI 1.19–1.62), houses with walls built using rudimentary materials (AOR = 1.38, 95% CI 1.04–1.83), at least 6 children living in the house (AOR 1.22, 95% CI 1.00–1.49), children being 1 or 2 years old was associated with increased odds (AOR 1.89, 95% CI 1.50–2.34 and AOR 1.89, 95% CI 1.52–2.36), children from households with only treated nets (AOR 1.23, 95% CI 1.04–1.46) and those from the North West or South East regions (AOR 1.50, 95% CI 1.10–2.05 and AOR 1.48, 95% CI 1.01–2.16), respectively. All other predictors were not associated with the risk of malaria.ConclusionThe factors associated with the risk of malaria in this study included sleeping under treated mosquito nets, the age of the children, residing in the northwest and southeast regions, wall construction material, 6 children and above in the household and hearing/seen malaria messages in the last 6 months. Continuous health education and public health interventions, such as the provision of LLITNs, will reduce the risk of malaria and improve the health and well-being of children under 5 years of age.