The microbial communities in two apple orchards were characterised using amplicon-based metabarcoding. Samples were taken from tree station locations along a linear transect and from adjacent grass aisles, at both orchards. Comparison was made between the communities occurring at tree station locations and the grass aisles, and between orchards. Further discussion of these datasets is given in https://doi.org/10.1016/j.apsoil.2018.05.015 (Deakin et al., 2018).