Phosphorus (P) availability in subtropical soils does not often meet the nutritional demand of native tree species such as the ipê-roxo tree (Handroanthus heptaphyllus); therefore, it is necessary to supply P at planting. However, the impact of P on root system growth remains unknown. The aim of the current study was to investigate the effect of P application on root morphology of H. heptaphyllus plants over a 36-month period in a subtropical climate region. During the experiment, the plants subjected to fertilization with 40 kg P ha−1 were compared to untreated control. Plant roots were scanned through minirhizotron system 18 and 36 months after transplant (MAT), and generated images were used to determine total root length, mean root diameter and total root volume. Plant height and leaf P concentrations were also evaluated. Phosphorus application enhanced root and whole plant growth with a more evident effect at 36 MAT, when soil P availability decreased. The results give important information on the cultivation of H. heptaphyllus plants in soils presenting low P availability.