Large inter-individual variability of activation strategies is observed during hamstring strengthening exercises but their consequences remain unexplored. The objective of this study was to determine whether individual activation strategies are related to the distribution of damage across the hamstring muscle heads semimembranosus (SM), semitendinosus (ST), and biceps femoris (BF) after eccentric contractions. 24 participants performed 5 sets of 15 maximal eccentric contractions of knee flexors on a dynamometer, while activation of each muscle head was assessed using surface electromyography. Knee flexion maximal isometric strength was assessed before exercise and 48 h afterward. Shear modulus was measured using shear wave elastography before exercise and 30 min afterward to quantify the distribution of damage across the hamstring muscle heads. At 48 h, maximal knee flexion torque had decreased by 15.9% ± 16.9% (p < 0.001). Although no differences between activation ratios of each muscle were found during the eccentric exercise (all p > 0.364), we reported a heterogeneous distribution of damage, with a larger change in shear modulus of ST/Hams than SM/Hams (+70.8%, p < 0.001) or BF/Hams (+50.3%, p < 0.001). A large correlation was found between the distribution of activation and the distribution of damage for ST/Hams (r = 0.69; p < 001). This study provides evidence that the distribution of activation during maximal eccentric contractions has mechanical consequences for synergist muscles. Further studies are needed to understand whether individual activation strategies influence the distribution of structural adaptations after a training program.