The control of several citrus diseases requires continuous applications of fungicides containing copper (Cu) which favor to the accumulation of this metal in the soil. Therefore, the evaluation of how nutrient availability and rootstock interact with Cu toxicity in the citrus trees is required to maintain sustainability of fruit production in Cu-contaminated soils. Valencia orange trees on Sunki mandarin (SM) or Swingle citrumelo (SC) rootstock were grown in nutrient solutions combining adequate Cu (1.0 μmol L−1), excess Cu (50.0 μmol L−1), deficient phosphorus (P) (0.01 mmol L−1) and sufficient P (0.5 mmol L−1). The excess Cu reduced root and shoot growth, chlorophyll and relative water content in the leaves of the trees compared to those under adequate Cu supply. Furthermore, excess Cu caused severe damage to the root ultra-structure, characterized by the degeneration of the middle lamella and the presence of a thin and sinuous cell wall, as well as, starch accumulation in the plastids, disruption of the mitochondrial membranes and cellular plasmolysis. The damage caused by excess Cu in the cell wall and middle lamella on the root cells of SC was less severe than SM. Sufficient P supply improved the structure of the cell wall and middle lamella of trees subjected to excess Cu in comparison to P-deficient ones. Thus, the occurrence of more preserved cell wall and middle lamella supports the idea that sufficient P availability in the rooting medium and the use of SC rootstock might contribute to increase the ability of young citrus trees to cope with Cu toxicity.