Small containers used in seedlings production of tree species with different root architecture can result in serious constraints for root growth and unsuitable plant quality, with potential impacts on field performance. We compare responses of root morphology to changes in container size and shape in both deep-rooting (Acacia caven) and shallow-rooting (Baccharis linearis) species, both commonly used in active restoration plans in central Chile. For both species, seedlings were cultivated in four different PVC container-types varying in size (440 mL and 880 mL) and shape ([10, 20, 35, and 45] cm in length), and a control treatment that consists in the commonly container-type used in Chilean nurseries (440 mL black polyethylene bag). Seedlings were cultivated for one growing season under controlled conditions and a set of above- and belowground morphological parameters were evaluated. A second short experiment was performed afterwards to evaluate potential seedling quality through the root growth potential (RGP) test. Results showed that an increase in container volume differently affected morphological parameters of A. caven and B. linearis seedlings. The control treatment had high presence of spiral roots for the deep-rooting species, restricting normal root growth. For both species, elongated containers (>35 cm) produced seedlings with smaller shoots with longer root systems and without deformations in the taproot or main root. Elongated containers also restarted growth of new roots more deeply in the container as result of the RGP test. We concluded that contrasting root architecture of native species require different container size in nursery to promote an adequate root development and growth.