Adaptive responses to abiotic stresses such as soil acidity in Eucalyptus—the most widely planted broad-leaf forest genus globally—are poorly understood. This is particularly evident in physiological and anatomical disorders that inhibit plant development and wood quality. We aimed to explore how the supply of Ca and Mg through liming (lime), combined with Cu and Zn fertilization (CZF), influences physiological and anatomical responses during Eucalyptus grandis seedlings growth in tropical acid soil. Therefore, related parameters of leaf area and leaf anatomy, stomatal size, leaf gas exchange, antioxidant system, nutrient partitioning, and biomass allocation responses were monitored. Liming alone in Eucalyptus increased specific leaf area, stomatal density on the abaxial leaf surface, and Ca and Mg content. Also, Eucalyptus exposed only to CZF increased Cu and Zn content. Lime and CZF increased leaf blade and adaxial epidermal thickness, and improved the structural organization of the spongy mesophyll, promoting increased net CO2 assimilation, and stomatal conductance. Fertilization with Ca, Mg, Cu, and Zn positively affects plant nutrition, light utilization, photosynthetic rate, and antioxidant performance, improving growth. Our results indicate that lime and CZF induce adaptive responses in the physiological and anatomical adjustments of Eucalyptus plantation, thereby promoting biomass accumulation.