Background: Argan (Argania spinosa) is an important arid species in Morocco, hence the need to undertake nursery practices that promote its regeneration and sustainability in a vulnerable environment. This study aimed to examine the effect of container size and growing medium on morphological traits, biomass, as well as root morphology of one-year-old argan seedlings in the Marrakech region of Morocco. Methods: Three container sizes of 300, 400, and 500 cm3 were selected in which seven types of growing media with varying proportions of acacia compost, crushed cypress cones, Barbary thuja, eucalyptus capsule composts, and potting soil were used. Subsequently, measurements of plant growth variables and biomass, as well as identification of root deformations were carried out. Results: Our results show that container size and growth medium strongly influenced (p < 0.001) morphological traits and biomass of argan seedlings. Growth was highest in seedlings grown in the 500 cm3 container on substrates composed of both 100% acacia compost and 50% potting soil + 50% acacia compost, while it was lowest in seedlings in the 300 cm3 container with the compost composed of a mixture of equal proportions of cypress and Barbary thuja, and eucalyptus. While the main root deformities were hooked roots (14.1%) and root eccentricity (13.0%), seedlings with multiple deformities were by far the most common (38.4%). The size of the container did not seem to influence their occurrence, whereas about 35% of the deformations were observed in seedlings grown on substrates composed of mixtures of potting soil and acacia compost, cypress cones, and Barbary thuja and eucalyptus composts. Conclusions: This study shows the importance of adopting an adequate protocol to allow the regeneration of forest species with the necessary characteristics to survive the often-challenging environmental conditions prevailing not only in southern Morocco but also across most of the country.