Tropical rainforests such as the Amazon are of high importance as a global carbon sink. Due to its well-known nutrient limitation, the Amazon rainforest relies heavily on rapid microbial decomposition of biomass to release freshly available nutrients for plant growth. Despite the fundamental importance of decomposers for this ecosystem, little is known about the biodiversity of such microbiomes, their functional activity, and spatial and seasonal variability. We used 16S rDNA and ITS rDNA sequencing to analyze the microbial communities of the Amazon’s terra firme and the much drier white-sand ecosystems during the dry and wet seasons in 2022. Bacterial microbiomes differed significantly between seasons, displaying lower bacterial species richness and diversity in response to seasonal drought. In contrast, fungal richness and diversity differed strongly between sites, but were less affected by seasonal variation, suggesting their hyphae network and associations with plants as potential protectors against drought effects. Fungal and bacterial communities alike showed lower abundance of taxa involved in organic matter decomposition following seasonal drought. These changes were also reflected at the functional level, with samples collected during the dry season and at white-sand sites featuring lower abundances of decomposition and denitrification pathways. Soil hydro-chemical data also emphasizes how prolonged drought may limit soil nutrient supply via local microbiomes. Our results suggest that the reduced nutrient availability and soil connectivity during drought and within the white-sand ecosystem lower microbial activity and functional redundancy, henceforth demonstrating a strong impact of ecosystem type and drought on tropical microbiomes and their functional capacities. Our results further highlight that the observed increase in droughts in the Amazon rainforest may additionally limit nutrient supply through the microbial community, limiting carbon sequestration in the ecosystem with negative consequences for the global climate system.