Recycling empty fruit bunches (EFBs) in mature oil palm stands usually consists in distributing them over a limited area representing 3%–10% of the plot. The impact of this practice on soil quality, including soil biodiversity, is not well known at the plot scale. We analysed soil physical, chemical, and biological variables. Five zones were defined around the palm tree to assess spatial heterogeneity due to plant cover and application of organic and inorganic fertilisers. Each zone was analysed separately. Our study revealed marked variations in mineral contents around the palm tree, ranging from deficiency to excess or nutrient imbalance in adjacent zones, particularly in available P and K, Mg and pH. Similar variations in macrofauna were observed both in the litter and the soil. Our results demonstrate that the changes caused by plant cover and applications of fertiliser are mainly limited in space, but that earthworm communities move as a function of variations in nutrient availability or stress associated with EFB deposition over time. The Amacher index, adapted to the soil nutrient status for oil palm, indicated that average mineral fertility at the plot scale was rather good. The average density of soil macrofauna and nematofauna was low compared to other tropical ecosystems, but reference data from Indonesia are lacking. Application of EFBs on the harvest path mainly improved the homogeneity of soil quality within the elementary plot around the palm. However these data did not show that recycling EFB stimulates soil fauna communities or carbon sequestration at the plot scale.