Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. After the first nine months of throughfall exclusion, prokaryotic communities showed no change in composition. However, 18 months of throughfall exclusion resulted in markedly divergent prokaryotic community responses, reflecting MAP and soil fertility. We observed the emergence of a “drought microbiome” within infertile sites, whereby the community structure of the experimental drying plots at the lower MAP sites diverged from their respective control sites and converged towards overlapping assemblages. Furthermore, taxa increasing in relative abundance under throughfall exclusion at the highest MAP became more similar to taxa characteristic of the control plots at the lowest MAP site, suggesting a shift toward communities with life-history traits selected 1