Excessive physical fatigue post-exercise triggers muscle performance decline and cellular damage due to free radical accumulation, necessitating safe, natural nutritional interventions as alternatives to synthetic stimulants. This study aimed to analyze the bioactive compound composition, antioxidant capacity, cellular bioenergetic recovery efficacy, and molecular docking mechanisms of fenugreek seed extract (Trigonella foenum-graecum L., TFGE). Methods involved dual-polarity UHPLC-Q Exactive HF-X LC-MS/MS metabolomic profiling, cell-free in vitro antioxidant assays, hydrogen peroxide (H2O2)-induced oxidative stress modeling in C2C12 skeletal muscle myoblasts, and molecular docking simulations using AutoDock Vina against Keap1 and AMPKα proteins. Analysis identified 20 major bioactive compounds, including trigonelline, 4-hydroxyisoleucine, orientin, vitexin, diosgenin, and quercetin. TFGE exhibited potent free radical scavenging activity in DPPH (EC50 = 0.038 mg/mL) and ABTS (EC50 = 0.042 mg/mL) assays. In H2O2-treated C2C12 myoblasts, TFGE treatment (40 µg/mL) restored cell viability from 51.4% to 88.6%, suppressed reactive oxygen species (ROS) and malondialdehyde (MDA) accumulation, and reactivated endogenous antioxidant enzymes (SOD, CAT, GSH-Px). Furthermore, TFGE replenished intracellular glycogen stores, accelerated lactate clearance, and restored membrane Na+-K+-ATPase and Ca2+-Mg2+-ATPase pump activities. Docking simulations confirmed robust binding interactions between TFGE constituents and the Keap1 Kelch domain (scores up to -9.6 kcal/mol) and AMPKα kinase domain (scores up to -8.2 kcal/mol). Physical fatigue post-exercise due to oxidative stress and bioenergetic depletion presents a major physiological challenge that requires targeted natural interventions. In conclusion, TFGE demonstrates significant in vitro cytoprotective and bioenergetic recovery effects, suggesting its potential as a nutraceutical candidate pending further in vivo validation.