Data comprise phytohormone concentrations (plant growth hormones: adenosine, zeatin, isopentenyladenosine, indole-3-acetic acid and abscisic acid) measured during plant growth experiments in soil and hydroponic growth media in the presence and absence of earthworms (Lumbricus terrestris and Eisenia fetida respectively). Also presented are plant biomass, pH of the hydroponic solution and soil biological activity (concentration of Fluorescein diacetate - a measure of the hydrolytic capacity) at the end of the study. The study was funded by the NERC (Grant number NE/M000648/1). Mass spectrometry was carried out in The York Centre of Excellence in Mass Spectrometry; the centre was created thanks to a major capital investment through Science City York, supported by Yorkshire Forward with funds from the Northern Way Initiative, and subsequent support from EPSRC (EP/K039660/1; EP/M028127/1).