This study aimed to characterise the biomechanics of the widely practiced eccentric heel-drop exercises used in the management of Achilles tendinosis. Specifically, the aim was to quantify changes in lower limb kinematics, muscle lengths and Achilles tendon force, when performing the exercise with a flexed knee instead of an extended knee. A musculoskeletal modelling approach was used to quantify any differences between these versions of the eccentric heel drop exercises used to treat Achilles tendinosis. 19 healthy volunteers provided a group from which optical motion, forceplate and plantar pressure data were recorded while performing both the extended and flexed knee eccentric heel-drop exercises over a wooden step when barefoot or wearing running shoes. This data was used as inputs into a scaled musculoskeletal model of the lower limb. Range of ankle motion was unaffected by knee flexion. However, knee flexion was found to significantly affect lower limb kinematics, inter-segmental loads and triceps muscle lengths. Peak Achilles load was not influenced despite significantly reduced peak ankle plantarflexion moments (p < 0.001). The combination of reduced triceps lengths and greater ankle dorsiflexion, coupled with reduced ankle plantarflexion moments were used to provide a basis for previously unexplained observations regarding the effect of knee flexion on the relative loading of the triceps muscles during the eccentric heel drop exercises. This finding questions the role of the flexed knee heel drop exercise when specifically treating Achilles tendinosis.