Purpose: Although the Achilles tendon (AT) is the largest and strongest tendon, it remains one of the most vulnerable tendons among elite and recreational runners. The present study aims to explore the effects of 12-week gait retraining (GR) on the plantar flexion torque of the ankle and the morphological and mechanical properties of the AT. Methods: Thirty-four healthy male recreational runners (habitual rearfoot strikers) who never tried to run in minimal shoes were recruited, and the intervention was completed (20 in the GR group vs. 14 in the control (CON) group). The participants in the GR group were asked to run in minimal shoes (INOV-8 BARE-XF 210) provided by the investigators with forefoot strike patterns during the progressive 12-week GR. Meanwhile, the participants in the CON group were instructed to run in their own running shoes, which they were familiar with, with original foot strike patterns and intensities. The morphological properties of the AT, namely, length and cross-sectional area (CSA), were obtained by using an ultrasound device. A dynamometer was utilized simultaneously to measure and calculate the plantar flexion torque of the ankle, the rate of torque development, the peak force of the AT, and the stress and strain of the AT. Results: After 12-week GR, the following results were obtained: (1) A significant time effect in the peak ankle plantarflexion torque was observed (p = 0.005), showing a 27.5% increase in the GR group; (2) A significant group effect in the CSA was observed (p = 0.027), specifically, the increase in CSA was significantly larger in the GR group than the CON group; (3) A significant time effect in the peak AT force was observed (p = 0.005), showing a 27.5% increase in the GR group. Conclusion: The effect of 12 weeks of GR is an increase in AT CSA, plantar flexor muscle strength of the ankle, and peak AT force during a maximal voluntary isometric contraction test. These changes in AT morphology and function could be positive for tendon health and could prevent future AT injury.