Myotendinous junctions (MTJs) are anatomical regions specialized in transmission of contractile strength from muscle to tendon and, for this reason, a common site where acute injuries occur during sport activities. In this work we investigated the influence of exercise intensity on MTJ plasticity, as well as on the expression of insulin-like growth factor 1 (IGF-1) and transforming growth factor beta (TGF-β) and their receptors in muscle and tendon. Three groups of rats were analyzed: control (CTRL), slow-runner (RUN-S) and fast-runner (RUN-F) trained using a treadmill. Ultrastructural and morphometric analyses of distal MTJs from extensor digitorum longus muscles have been performed. Contractile strength and hypertrophy were investigated by using in vivo tension recordings and muscle cross-sectional area (CSA) analysis, respectively. mRNA levels of PGC-1α, vinculin, IGF-1Ea and TGF-β have been quantified in muscle belly, while IGF-1Ea, TGF-β and their receptors in tendon. Morphometry revealed an increased MTJ complexity and interaction surface between tissues in trained rats according to training intensity. CSA analysis excluded hypertrophy among groups, while muscle strength was found significantly enhanced in exercised rats in comparison to controls. In muscle tissue, we highlighted an increased mRNA expression of PGC-1α and vinculin in both trained conditions and of TGF-β in RUN-F. In tendon, we mainly noted an enhancement of TGF-β mRNA expression only in RUN-F group and a raise of Betaglycan tendon receptor mRNA levels proportional to exercise intensity. In conclusion, MTJ plasticity appears to be related to exercise intensity and molecular analysis suggests a major role played by TGF-β.