Phenotypic plasticity in response to environmental variation occurs at all organizational levels and across temporal scales within plants. However, the magnitude and functional significance of this plasticity is little explored in perennial species. We examined the influence of different light regimes and nitrogen (N) availability on the morphological and physiological plasticity of coffee seedlings (Coffea arabica L.). Potted plants were grown under full sunlight and shade (50%) and were fertilized with Hoagland’s solutions containing 0, 16 or 23mM N. Most leaf traits responded to light with a classic full sunlight vs. shade dichotomy [e.g., compared with those grown under full sunlight, 50% leaves had a thinner palisade mesophyll and a lower leaf mass per area (LMA) for improved light capture]. The outer periclinal cell walls in both epidermises exhibited thick epicuticular wax and three distinct layers. Chloroplasts of the mesophyll cells were densely occupied by thylakoids and starch grains. These characteristics were observed most clearly in plants supplemented by nitrogen or in those grown in shade conditions. Large starch granules were observed, but no membrane injuries were observed in either treatment. The plasticity index was high for the physiological traits that are associated with photoprotection and the maintenance of a positive carbon balance under shade but was low for most morpho-anatomical features.