Quality pecan rootstocks that ensure genetic and phytosanitary safety, besides having good vegetative development, are extremely important to implant a successful orchard. Rootstocks with vigorous radicular systems affect plant growth. This study aimed at evaluating rootstock growth as the result of root pruning and the use of different containers to grow pecan rootstocks in an organic system. The experiment was conducted with “Barton” rootstocks in the experimental area at the Embrapa Clima Temperado in Pelotas, RS, Brazil, in 2018, 2019 and 2020. Rootstocks were evaluated in plastic bags and tubes and in the soil, associated with root pruning. Evaluation 280 and 480 days after transplant comprised the following: height of the aerial part, length of primary and secondary radicular systems, stem diameter, leaf area, dry mass of the aerial part, dry mass of the radicular system, dry mass of secondary roots and the Dickson Quality Index. The use of plastic bags to produce pecan rootstocks was found to coil roots at the bottom of the container. Neither containers nor root pruning affected stem diameter, an important parameter to carry out grafting. Pecan rootstocks with a non-pruned radicular system grown in plastic bags developed large main root and aerial part. Pruning of pecan radicular systems in containers and in the soil leads to increase in the number of main roots but decreases root length.