The purpose of this study was to examine the skeletal muscle hypertrophic, architectural, and performance-related adaptations in response to volume-matched, total-body flywheel versus traditional resistance training in a randomized, non-exercise controlled study in physically active young adults. Thirty-one healthy young adults (24 ± 3 y) were randomized to 10 weeks of traditional resistance training (TRT; n = 7F/5M), flywheel training (FWRT; n = 7F/4M), or a habitual activity control (CON; n = 5F/3M). Maximal voluntary isometric torque (MVIT), one repetition-maximum (1RM) for the free weight squat and bench press, three repetition work maximum (3Wmax) for the flywheel squat and bench press, countermovement jump height, and broad jump distance, as well as site-specific muscle hypertrophy, fascicle length (FL), and pennation angle, were measured. Both TRT and FWRT increased MVIT (p ≤ 0.021) and FFM (p ≤ 0.032) compared to CON. However, TRT promoted superior improvements in free weight squat and bench 1RM (p < 0.001), and FWRT improved flywheel 3Wmax squat and bench (p < 0.001). FWRT increased the FL and cross-sectional area of the distal VL, countermovement jump height, and broad jump distance (p ≤ 0.048), whereas TRT increased the pennation angle and cross-sectional area of the proximal VL. Therefore, 10 weeks of volume-matched, total-body traditional, and flywheel resistance training similarly increased maximal isometric strength and fat-free mass. However, FWRT promoted unique skeletal muscle architectural adaptations that likely contributed to region-specific VL hypertrophy and jump performance improvements. Thus, FWRT provides a novel training stimulus that promotes architectural adaptations that support improved athletic performance in a manner that is not provided by traditional resistance exercise training.