Despite the dramatic changes in land-use arising from expansion of the palm oil industry, soil biodiversity in oil palm plantations has been little investigated. The present study aims to assess the effect of organic waste recycling (empty fruit bunches, EFB) on soil biodiversity in a mature plantation in Sumatra, Indonesia. A chronosequence was delineated taking into account the time between the applications of EFB and soil sampling; intervals of 1, 3, 6, 12, 18 and 24 months were compared with control plots without EFB application. Soil physical and chemical characteristics and macrofauna and nematofauna populations were analysed. The findings highlighted three distinct periods: a first disturbance period (0-6 months) showing a marked increase in pH, potassium content, base saturation and macrofauna abundance, especially ants, whereas earthworm, millipede and nematode populations were substantially reduced; a resilience period (6-18 months); and a final period (18-24 months) showing an improvement in most soil fertility parameters and a high density of earthworms, millipedes and nematodes. The impact of EFB application on soil quality changed as a function of time, and the present results explain the apparent discrepancy of some previous published results. This research is the first stage towards developing new strategies for enhancing soil biodiversity and related services for sustainable oil palm cultivation.