ABSTRACT OBJECTIVE To analyze the environmental and socioeconomic risk factors of malaria transmission at municipality level, from 2010 to 2015, in the Brazilian Amazon. METHODS The municipalities were stratified into high, moderate, and low transmission based on the annual parasite incidence. A multinomial logistic regression that compared low with medium transmission and low with high transmission was performed. For each category, three models were analyzed: one only with socioeconomic risk factors (Gini index, illiteracy, number of mines and indigenous areas); a second with the environmental factors (forest coverage and length of the wet season); and a third with all covariates (full model). RESULTS The full model showed the best performance. The most important risks factors for high transmission were Gini index, length of the wet season and illiteracy, OR 2.06 (95%CI 1.19–3.56), 1.73 (95%CI 1.19–2.51) and 1.10 (95%CI 1.03–1.17), respectively. The medium transmission showed a weaker influence of the risk factors, being illiteracy, forest coverage and indigenous areas statistically significant but with marginal influence. CONCLUSIONS As a disease of poverty, the reduction in wealth inequalities and, therefore, health inequalities, could reduce the transmission considerably. Besides, environmental risk factors as length of the wet season should be considered in the planning, prevention and control. Municipality-level and fine-scale analysis should be done together to improve the knowledge of the local dynamics of transmission.