Soil drainage and phosphorus (P) availability are considered indicators of management intensity in pasture-based agriculture supporting livestock. However, microbial adaptations to P-availability according to soil drainage class are rarely investigated. We hypothesized that well-drained grasslands with high P-availability will sustain a distinctive soil microbiota when compared to poorly-drained grasslands with low-P availability. The relationship between soil drainage, plant available P and grassland microbial communities was evaluated among well-drained sites with high- or low-P and poorly-drained sites with high- or low-P, using fingerprinting, next-generation sequencing and quantitative PCR. Bacterial community structures were primarily affected by drainage as well as significantly separated between a combination of drainage and P availability i.e. low-P and poorly drained versus high-P and well drained. Abundance of the bacterial phylum Actinobacteria was significantly higher in well-drained high-P soils while Firmicutes were more abundant in well-drained low-P soils. Soil fungal communities responded to both drainage status and plant available P. Fungal phyla such as Basidiomycota responded strongly towards availability of P, while Glomeromycota were most abundant in poorly drained low-P soils. The diversity of the alkaline phosphatase gene phoD responded more clearly to drainage than availability of P. Of the other environmental factors, soil pH significantly affected the bacterial and fungal communities structure analyzed. This study suggests that while bacteria and fungi are affected by a combination of soil drainage and P availability in Irish grassland soils, drainage has a more profound influence on bacterial communities than P availability.