Conserving the remaining savanna ecosystems in the Brazilian savanna (Cerrado) — a global biodiversity hotspot that stores carbon and provides water to a large portion of South America — requires understanding the ecological processes maintaining their function. Nutrient cycling supports savanna function via plant litter production and decomposition by soil fauna, releasing nutrients for plant and soil organism uptake. Soil biodiversity and biogeochemistry linkages with litter dynamics in Neotropical savannas under a changing climate are poorly understood. Here, we combined two years of rainfall seasonality, leaf and wood litter production and decomposition with soil epigeic fauna abundance — the number of ground-surface dwelling invertebrates collected through pitfall traps — taxa richness, Shannon’s diversity and Pielou’s evenness, and 16 soil biogeochemical variables measured in 12 plots of preserved savanna. Rainfall seasonality modulated the mean soil epigeic fauna diversity and evenness across all plots, which were highest in the rainy season, in contrast to litterfall rates, which peaked in the dry season. In the dry season (April to September), the Formicidae family was the most abundant with 50% of all individuals, while in the rainy season (October to March), the Isoptera order was the most abundant with approximately 39% of individuals. Wood litter decomposition grouped with annual Hemiptera abundance, co-varying with soil epigeic fauna diversity and evenness per plot and against soil fertility variables. Leaf litter decomposition co-varied with the total epigeic fauna abundance and soil pH. We speculate that the specific need to decompose wood litter may be associated with a greater need for diversity than an abundance of soil epigeic fauna. Our work highlights the role of rainfall seasonality on soil biodiversity and physicochemistry, which is also tightly linked with litter production and decomposition. This study advances our understanding of the mechanisms governing nutrient cycling in savanna ecosystems on nutrient-impoverished soils, with implications for achieving sustainable conservation and restoration goals.