This set of data describes protozoa abundance and diversity in samples taken at the Sourhope experimental site in 1999 and 2000 by the Centre for Ecology & Hydrology and the University of Glasgow. Data were collected during a project funded under the NERC Soil Biodiversity Programme. The NERC Soil Biodiversity Thematic Programme was established in 1999 and was centred upon the intensive study of a large field experiment located at the Macaulay Land Use Research Institute (now the James Hutton Institute) farm at Sourhope in the Scottish Borders (Grid reference: NT8545019630). During the experiment, the site was monitored to assess changes in above-ground biomass production (productivity), species composition and relative abundance (diversity). Full details about this dataset can be found at https://doi.org/10.5285/a5737c31-5c8d-43f3-980a-4736510d6b05