Aims: Tree logging in tropical tree plantations results in significant soil disturbances that negatively impact soil biodiversity and soil functioning. Here, we aimed to assess the effects of adding organic matter (OM) to soil after rubber tree logging on soil functioning over time. Methods: The experiment was conducted in two contrasting soil types in Ivory Coast. Four practices were replicated, including a control with no residues, the presence of legumes only, legumes and all tree parts excluding the trunk, and legumes and all the parts of the tree including the trunk. We monitored the response of soil nematode communities every six months for 24 months in each practice. Samples were collected from the topsoil layer (0–10 cm) in the interrow, and we also monitored soil carbon transformation by measuring in situ basal soil respiration, labile soil carbon and organic matter decay using the bait lamina method. Results: The results showed a sharp decrease in nematode abundance after tree logging, but OM restoration increased nematode abundance, the relative abundance of bacterivores, and resource availability to the soil food web. The resilience of the nematode communities depended on soil conditions and the amount and quality of logging residues. Total nematode abundance was positively and significantly related to soil functioning, measured through basal soil respiration, labile soil carbon, and organic matter decay rate. Conclusion: The results suggest that restoring logging residues can be an effective way to restore soil biodiversity and mitigate the negative impact of clear-cutting in tropical rubber plantations.