Purpose <p>Nanotechnology has been considered a feasible technology to reduce contamination and ensure food security. Molybdenum oxide nanoparticles (NPMo) show “low volume and high efficiency” characteristics in agriculture, indicating great potential for agricultural field. Therefore, the study of the availability and morphological transformation of NPMo in soil is extremely meaningful for the sustainable development of nano-agrochemicals.</p> Materials and methods <p>Batch and soil incubation experiments were conducted with Mo-deficient acidic yellow-brown soil, and two Mo fertilizers (ammonium molybdate, IMo; and NPMo) were used to investigate the isothermal adsorption and transformation characteristics of NPMo and its differences with IMo.</p> Results and discussion <p>The results indicated that pH and phosphorus additions affected soil adsorption of NPMo as much as IMo, with higher adsorption in the range of pH 1–4 and a sharp decrease in molybdenum adsorption as the level of exogenous phosphorus additions was increased; moreover, NPMo adsorption was lower in soils as compared to IMo. Exogenous Mo causes a redistribution of soil Mo morphology towards the weakly crystallized ferromanganese-conjugated state of Mo and that Al₂(MoO₄)₃ was the predominant assemblage in soil. Meanwhile, compared to IMo, NPMo treatment had higher Mo content extracted with chemical reagent.</p> Conclusions <p>NPMo can reduce the adsorption and immobilization of Mo in acidic yellow-brown soil compared to IMo, thus increasing the availability of Mo.</p>