Nickel hyperaccumulator plants play a major role in nickel recycling in ultramafic ecosystems, and under agromining the nickel dynamics in the farming system will be affected by removal of nickel-rich biomass. We investigated the biogeochemical cycling of nickel as well as key nutrients in an agromining operation that uses the metal crop Phyllanthus rufuschaneyi in the first tropical metal farm located in Borneo (Sabah, Malaysia). For two years, this study monitored nine 25-m2 plots and collected information on weather, biomass exportation, water, and litter fluxes to the soil. Without harvesting, nickel inputs and outputs had only minor contributions (<1 %) to the total nickel budget in this system. The nickel cycle was mainly driven by internal fluxes, particularly plant uptake, litterfall and throughfall. After two years of cropping, the nickel litter flux corresponded to 50 % of the total nickel stock in the aerial biomass (3.1 g m-2 year-1). Nickel was slowly released from the litter; after 15 months of degradation, 60 % of the initial biomass and the initial nickel quantities were still present in the organic layer. Calcium, phosphorus and potassium budgets in the system were negative without fertilisation. Unlike what is observed for nickel, sustained agromining would thus lead to a strong depletion of calcium stocks if mineral weathering cannot replenish it.