The data consist of standardised counts of taxon abundances (bacteria, fungi and micro eukaryotes) from soil samples collected from paired intensive and extensive grassland systems, including low and high pH parent soils, from 32 sites across the United Kingdom. The samples were collected during winter and spring 2015-2016 from sites across the UK. DNA were extracted and taxonomic marker genes assessed using high-throughput DNA sequencing techniques to yield information about the genetic diversity and abundance of the microorganisms therein. The data were collected to help understand soil functional change in a variety of management and climatic scenarios as part of NERC U-GRASS (Understanding and enhancing soil ecosystem services and resilience in UK grass and croplands) award (NERC Reference NE/M017125/1) part of the NERC Soil Security Programme.