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Abstract We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El‐Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter antAtta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post‐drought the microbiomes were similar to pre‐drought conditions, demonstrating the resilience of soil microbial communities to drought events.A. cephalotesnests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post‐drought. Drought increased CH₄consumption in soils due to lower soil moisture, andA. cephalotesnests decrease the variability of CH₄emissions in some soil types. CH₄emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.