The primary aim of the present study was to analyze mechanical responses during inertial knee-and hip-dominant hamstring strengthening exercises (flywheel leg-curl and hip-extension in conic-pulley), and the secondary aim was to measure and compare regional muscle use using functional magnetic resonance imaging. Mean power, peak power, mean velocity, peak velocity and time in the concentric (CON) and eccentric (ECC) phases were measured. The transverse relaxation time (T2) shift from pre-to post-exercise were calculated for the biceps femoris long (BFl) and short (BFs) heads, semitendinosus (ST) and semimembranosus (SM) muscles at proximal, middle and distal areas of the muscle length. Peak and mean power in flywheel leg-curl were higher during the CON than the ECC phase (p<0.01). ECC peak power was higher than CON phase (p<0.01) in conic-pulley hip-extension exercise, while mean power was higher during the CON than ECC phase (p<0.01). Flywheel leg-curl showed a higher T2 values in ST and BFs and BFl (p<0.05), while the conic-pulley hipextension had a higher T2 values in the proximal region of the ST and BFl (p<0.05). In conclusion, ECC overload was only observed in peak power during the conic-pulley hip-extension exercise. Flywheel leg-curl involved a greater overall use of the 4 muscle bellies, more specifically in the ST and BFs, with a selective augmented activity (compared with the conic-pulley) in the 3 regions of the BFs, while conic-pulley hip-extension exercise selectively targeted the proximal and medial regions of the BFl. Physiotherapists and strength and conditioning coaches should consider this when optimizing the training and recovery process for hamstring muscles, especially after injury.