Cloudberry has good economic potential for Canada, but crop practices must be improved before commercial production can be established. Transplants usually consist of rhizome segments collected in natural populations; however, the very low root density of these transplants might partly explain their initial slow growth and high mortality. The objective of this study was to determine the effects of mineral fertilization and auxin applications on root initiation and elongation. Three N–P–K fertilization treatments were applied at the planting of bare rhizomes in peatlands, while auxin applications were tested in both greenhouse and field experiments. Roots of fertilized plants were two to four times longer and more numerous than those of control plants after one complete growing season but fertilization did not lead to early rooting. Rhizome segments produced new shoots before investing in root production, suggesting that rhizome carbohydrate reserves are not sufficient to allow both the shoot and root to be produced at the same time. Auxin applications to the rhizomes incurred high mortality and did not stimulate root production in both the field and greenhouse experiments. We conclude that fertilizers applied at planting can improve cloudberry initial survival rate, rooting, and early shoot growth, which could eventually lead to improved plant cover and fruit yield.