Eucalyptus is one of the most commonly planted genera worldwide for commercial timber purposes. Brazil has approximately 25% of the total Eucalyptus spp. planted worldwide. However, nutritional disorders caused by copper (Cu) and zinc (Zn) deficiencies have been more frequent in Eucalyptus plantations. Furthermore, the scientific knowledge regarding micronutrient fertilization is scarce. Sequential extraction can determine the distribution of metals in the soil, giving an order of magnitude to its bioavailability. The present study aimed to assess the soil Cu and Zn pools and evaluate the effects of mineral Cu and Zn fertilization on the nutritional status and nutrient fractionation in a Ferralsol in a cultivated Eucalyptus grandis plantation. The study considered two conditions—namely, forest residue management or removal of forest residues. The treatments included complete fertilization, no application of Cu, no application of Zn, maintenance of forest residues, and total removal of forest residues. High quantities of Cu and Zn were found in the soil, mainly in the low plant-available forms (>60%). There were no differences in the nutritional status of the trees, despite the absence of Cu and Zn via fertilizers and the removal of harvest residues. Foliar Cu concentration was positively correlated with soil exchangeable and oxide-bound Cu content, whereas foliar Zn concentration was positively correlated with soil exchangeable and organic matter-bound Zn content. The access to moderately labile forms of Cu and Zn by eucalypts may justify the absence of response to mineral fertilization, especially in areas where forest residues remain on the soil, and consequently, work as a source of Cu and Zn.