Purpose: This study aimed to determine whether an increase in muscle shear modulus measured 30 min after eccentric exercise (30 min) reflects the magnitude of force deficit measured 48-h post-exercise (48 H). Methods: A total of 53 healthy participants were distributed in five groups. Four groups performed either repeated eccentric elbow flexions or knee extensions at either a low or high load. A fifth group performed repeated concentric elbow flexions (control load). Results: A significant decreased peak torque was found for elbow flexors and knee extensors 48 h after the eccentric exercises (all P values < 0.001). A significant increase in shear modulus was found at 30 min for the elbow flexors for low (+70.5 ± 44.3%, P < 0.001) and high load (+153.9 ± 192.4%, P < 0.001). Similarly, the shear modulus of knee extensors increased for low (+26.7 ± 19.1%, P < 0.001) and high load (+79.4 ± 67.1%, P < 0.001). The relative increase in shear modulus measured at 30 min was significantly correlated to the relative decrease in peak torque measured at 48 H for both elbow flexors (r = −0.80) and knee extensors (r = −0.82). A further analysis suggested that biceps brachii and rectus femoris were more affected by muscle damage than their synergists. Conclusion: This study shows that an increase in muscle shear modulus measured 30 min after a damaging exercise reflects the decrease in peak torque measured at 48 H. Shear modulus may therefore, provide a useful tool for coaches and clinicians to non-invasively estimate the amount of muscle damage induced by a damaging exercise.