Aims This study investigated the physico-geochemical properties of three types of ultramafic substrates in Sabah (Malaysia) and further characterised their influence on nickel (Ni) accumulation in two selected tropical ‘metal crops’ (Phyllanthus rufuschaneyi and Rinorea cf. bengalensis). Methods Three experiments, consisting of a randomised block growth trial in large pots over 12 months in Sabah, were conducted: i) soil ratio experiment (Cambisol:Ferralsol:Leptosol), ii) soluble Ni dosing experiment with added 0, 60, 240, 600 mg Ni kg−1, and iii) soil pH adjustments (pH 5.2, 5.8 and 6.4) experiment. Results The results show that the low pH status of Ferralsol did not result in increased extractable Ni concentrations, indicating that Ni-bearing phases and mineralogy play a major role in Ni extractability in these substrates. The increasing order of extractable Ni concentrations was Ferralsol < Leptosol < Cambisol. The selected ‘metal crops’ had remarkable shoot biomass (~40 g pot−1) and foliar Ni concentrations (>15 g kg−1 in P. rufuschaneyi) in the Cambisol, >5-fold higher relative to that recorded in Leptosol and Ferralsol. Mixing the Cambisol with the other substrates significantly improved Ni yield in both species relative to the individual substrates. The effect of Ni addition on the selected ‘metal crops’ was species-dependent, whereas reduction of soil pH in Cambisol significantly reduced Ni yield in both species. Conclusions Nickel accumulation patterns in ‘metal crops’ in response to the diverse ultramafic soils in the tropics are influenced by the physico-geochemical characteristics of the soil types. Soil Ni extractability in these soils is more dependent on the Ni-bearing phases and mineralogy rather than the pH status. This study provides useful information on plant-soil interactions required for identifying suitable substrates for implementing tropical Ni agromining.