The production of argan seedlings in nurseries is considered a crucial step for the success of any argan forest regeneration program since it increases the rate of survival and growth. Therefore, the substrate and container play a vital role in argan seedling production, while the use of shade may improve soil moisture and decrease the water stress of the plant. This study aims to determine the effects of these factors and their interactions. For this, the effects of four shade levels (0%, 20%, 40%, and 80%) and six different compositions of the substrate, as well as four different sizes and forms of containers, on argan seedling production were studied for six months under greenhouse conditions, based on analyzing the leaf mineral elements and measuring morphological traits. According to the studied parameters, the results show that 0% and 40% of shade are, respectively, the best shade levels for growth, while the germination rate is higher only in an unshaded compartment (85.28%). Furthermore, the substrate based on peat moss lead to one of the higher germination rates (78.75%) and the finest plants in terms of chlorophyll content, and shoot and root growth, while the largest container (C2) had the best shoot and root growth with 34.34 cm of root length. However, the mineral analysis, mainly the leaf total nitrogen concentration, is correlated with morphological traits. In addition, the cost–benefit analysis study confirmed this finding and valorizes the use of S1 substrate (1/2 black peat and 1/2 blond peat) and a C2 container (volume: 3100 mL) since it is considered the most efficient and economic combination for different shade levels.