This resource comprises abundance data for invertebrates, pest damage to apples, and yields from an agroforestry system subject to two different understorey management treatments, comprising an unmown flowering understorey and a mown understorey. The data was collected from an intercropped apple-arable agroforestry site in Screveton, Nottinghamshire, UK, from five experimental blocks, each block split between the two understorey management treatments. The data was collected between April and September 2020. Data was collected using (i) pitfall traps, (ii) sticky traps, (iii) visual searches of apple trees for natural enemies, pests and fruit damage from pests and disease, (iv) flower visitation counts for pollinators, (v) apple fruit yield and quality metrics, and (vi) grain yield samples. The data was collected to compare the effect of understorey management in agroforestry on functional invertebrates and associated ecosystem services. All data was collected by Tom Staton (University of Reading). Three pitfall traps were damaged and are excluded from the dataset, comprising (i) Visit 1, Block 2, Mown treatment, Position 4; (ii) Visit 4, Block 2, Mown treatment, Position 3; and (iii) Visit 4, Block 3, Unmown treatment, Position 2. The research was funded under NERC grant NE/R012229/1 Quantitative and Modelling Skills in Ecology and Evolution (QMEE) CDT Full details about this dataset can be found at https://doi.org/10.5285/83a10b11-23ef-4378-a56d-c63cce365275