Weed control is a key aspect affecting seedling response in newly-established plantations. Tree shelter protection may be an effective complement to weed control with a positive effect on the overall response of seedlings. Our study focused on assessing the morpho-physiological response of Holm oak (Quercus ilex L. ballota [Desf.] Samp.) plantations to weed control and individual protection as a combined cultural technique on a cropland site in southern Spain. The weed control treatments (cultivation, herbicide and mulch) were also applied in combination with tree shelters. Morpho-physiological variables including survival, aerial and root morphology, water potential, gas exchange and chlorophyll fluorescence were monitored over a 2-year period. Results showed that weed competition management treatments improved the seedling survival rate compared to the control treatment. Moreover, shelter protection was proven to enhance the height growth of seedlings. At early stages of establishment, and particularly under combined treatments, all plants invested more resources in their aerial parts than in their root system. Seedlings did not regulate water loss as a result of water stress, contrary to the expectations in Mediterranean areas. Under all treatments, especially those combined with tree shelters, seedlings took up to 2 years to achieve morpho-physiological adaptation to site conditions, in terms of height and diameter growths, and water stress behavior. In addition, tree shelters promoted an increase in net photosynthesis compared to non-shelter treatments during the winter period. Tree shelters also limited the emergence of photo-inhibition phenomena in seedlings so that plants under combined treatments showed greater photo-chemical efficiency. Thus, this study supports the effectiveness of tree shelter protection as a complement to weed control treatments. More specifically, a combination of individual protection (shelter) and weed control around seedlings is an interesting technique for reforestation of agroforestry systems in the Mediterranean area.