The production of high-quality seedlings and their use in commercial planting reduce pressure on natural areas. Eugenia dysenterica DC is a native fruit tree from the Brazilian Cerrado, whose nutritional requirements are still unclear. This study aimed to evaluate the effects of nitrogen (N) and phosphorus (P) supplementation on the physiology, growth and nutrient uptake, and use efficiencies of E. dysenterica seedlings grown in glasshouse conditions. The following rates were used in separate experiments: 0, 50, 100, 200, and 400 mg dm−3 N and 0, 100, 200, 400, and 600 mg dm−3 P. The experiment was conducted in a randomized block with four replications. The lowest N rate (50 mg dm−3) increased the stomatal conductance (gS) and, consequently, resulted in the highest transpiration (E), electron transport (ETR), and photosynthetic (A) rates. Also, rates of 50 mg dm−3 and 100 mg dm−3 N increased the Root Uptake Efficiency (RUE) and plant Nutrient Use Efficiency (NUE) for macronutrients and the RUE for micronutrients, stimulating plant growth. Phosphorous fertilization resulted in the maximum values for photosynthesis, electron transport rate, total dry mass, and NUE at the 200 mg dm−3 rate. The results of this study suggest that fertilization with 50 mg dm−3 N and 200 mg dm−3 P is suitable for the development of E. dysenterica seedlings.