Research Highlights: Environmental abiotic stressors generate secondary stresses in plants, such as osmotic and oxidative stresses, which negatively influence their normal growth, development, and metabolism. Research about other non-enzymatic components with antioxidant capacity has recently focused on polyphenols. However, their role as indicators of drought and shade tolerance in woody species leaves and roots has been poorly explored or was limited to leaves only. Background and Objectives: Under a scenario of increasing drought, understanding the seedling responses in terms of total polyphenols and their antioxidant activity, in particular at the fine root system level, may help to elucidate the native–alien species interaction. Materials and Methods: At the beginning of July, 5-month-old native Quercus robur and alien Quercus rubra seedlings were transferred indoors to the growth chamber and subjected to progressive soil drying for 21 days. Results: The decrease in soil water content was more pronounced for Q. robur (9%) than for Q. rubra (34% of field capacity). Leaf water potential significantly decreased over time in Q. robur but did not differ from the control in Q. rubra. The total polyphenol concentration in Q. robur was markedly lower in the leaves and significantly higher in the fine roots than in Q. rubra. For the leaves, both species showed markedly higher values if well-watered, and the values significantly decreased in response to drought only in Q. rubra. In contrast, the fine root values for both species were markedly higher if droughted and decreased significantly in time only in Q. robur. Differently from the polyphenol concentration, the antioxidant capacity of Q. rubra was always higher in both the leaves and fine roots. Conclusions: The higher antioxidant activity of the alien species Q. rubra revealed by this work, combined with its isohydric behaviour, could further shed some light on our understanding of its competitive performance at the seedling stage against the native Q. robur.