Developing efficient crop fertilization practices has become more and more important due to the ever-increasing global demand for food production. One approach to improving the efficiency of phosphate and urea fertilization is to improve their interaction through nanocomposites that are able to control the release of urea and P in the soil. Nanocomposites were produced from urea (Ur) or extruded thermoplastic starch/urea (TPSUr) blends as a matrix in which hydroxyapatite particles (Hap) were dispersed at ratios 50% and 20% Hap. Release tests and two incubation experiments were conducted in order to evaluate the role played by nanocomposites in controlling the availability of nitrogen and phosphate in the soil. Tests revealed an interaction between the fertilizer components and the morphological changes in the nanocomposites. TPSUr nanocomposites provided a controlled release of urea and increased the release of phosphorus from Hap in citric acid solution. The TPSUr nanocomposites also had lower NH3 volatilization compared to a control. The interaction resulting from dispersion of Hap within a urea matrix reduced the phosphorus adsorption and provided higher sustained P availability after 4 weeks of incubation in the soil.