Minimalist shod runners have reported greater material and mechanical properties of the Achilles tendon (AT) due to increased loading than runners who wear more cushioned running shoes. This study aimed to investigate the effects of 12-week transition training from conventional shoes to minimalist shoes on AT loading in habitual rearfoot strike runners. Seventeen healthy male habitual rearfoot strikers completed 12-week transition training. They were instructed either to run in minimalist shoes with a forefoot strike pattern (MIN + FFS, n = 9) or run in minimalist shoes but were free to develop their strike pattern (MIN, n = 8). Ultrasound images were captured to determine the cross-sectional area of the AT. Sagittal plane ankle kinematics and ground reaction forces were recorded simultaneously to quantify ankle joint mechanics and AT loading. The strike angle significantly decreased in MIN + FFS after the transition training, indicating a flatter foot at initial contact, whereas no changes were observed in MIN. After training, a significant increase in peak plantarflexion moment was observed for MIN + FFS (15.4%) and MIN (7.6%). Significantly increased peak AT force, peak loading rate and peak stress were observed after training in both groups. Specifically, MIN + FFS had a greater increase in peak AT force (20.3% versus 10.1%), peak loading rate (37.2% versus 25.4%) and peak AT stress (13.7% versus 8.1%) than MIN. Furthermore, for both groups, there were no significant differences in the moment arm and cross-sectional area of the AT observed before and after 12 weeks of training. The results of this study suggested that it was insufficient to promote the morphological adaptation of the AT, but the mechanical loading of the AT was adapted during running after 12-week transition training with minimalist shoes in MIN + FFS and MIN. Preliminary evidence showed that a gradual transition to minimalist shoes with a forefoot strike pattern may be beneficial to the mechanical loading of the AT.