Running overuse injuries result from an imbalance between repetitive loadings on the anatomical structures and their ability to adapt to these loadings. Unfortunately, the measure of these in-vivo loadings is not easily accessible. An optimal amount of movement variability is thought to decrease the running overuse injury risk, but the influence of movement variability on local tissue loading is still not known. A 3D dynamic finite element foot model driven by extrinsic muscle forces was developed to estimate the stress undergone by the different internal foot structures during the stance phase. The boundary conditions of different trials with similar running speed were used as input. Variability in bone stress (10%) and cartilage pressure (16%) can be expected while keeping the overall running speed constant. Bone and cartilage stress were mainly influenced by the muscle force profiles rather than by ground reaction force. These findings suggest, first, that the analysis of a single trial only is not representative of the internal tissue loadings distribution in the foot and second, that muscle forces must be considered when estimating bone and cartilage loadings at the foot level. This model could be applied to an optimal clinical management of the overuse injury.