Nitrogen (N) fertilization promotes morphofunctional attributes that enhance plant performance under stress conditions, but the amount and form supplied modify the magnitude of plant responses. We assessed several morpho-physiological and biochemical responses of Prosopis laevigata seedlings to a high supply of N, provided as either inorganic (NH4NO3) or organic (amino acids). Such N treatments were applied on four-month-old seedlings as a supplement of 90 mg N to a regular supply of 274 mg N plant−1. Nitrogen supply modified biomass allocation patterns between leaves and roots regardless of N form. Increased N input decreased photosynthetic capacity, even when plants had high internal N reserves. Organic N fertilization reduced the N use efficiency, but increased leaf and root amino acid concentrations. Proteins accumulated in stems in plants receiving inorganic N, while the organic N increased leaf proteins. High N supply promoted root starch accumulation irrespective of N form. Nitrogen supply did not directly influence plants’ regrowth capacity. Still, resprouting was correlated to initial root-to-shoot ratios and root starch, confirming the importance of roots as storage reserves of starch for recovering biomass after browsing. These findings have practical implications for designing nutritional management strategies in nurseries to improve seedling performance in afforestation efforts.