While the number of studies investigating Achilles tendon pathologies has grown exponentially, more research is needed to gain a better understanding of the complex relation between its hierarchical structure, mechanical response, and failure. At the microscale, collagen fibers are, with some degree of dispersion, primarily aligned along the principal loading direction. However, during tension, rearrangements and reorientations of these fibers are believed to occur. As 3D micro-movements are hard to capture, the precise nature of this fiber reorganization remains unknown. This study aimed to visualize and quantify the intricate fiber changes occurring within rat Achilles tendons under tension. Rat tendons were in situ loaded with concurrent synchrotron phase contrast microCT imaging. The results are heterogenous and show that collagen fibers’ response to loading is nonuniform and depends on anatomical orientation. Furthermore, damage propagation could be visualized, revealing that in the presence of heterotopic ossification, damage proceeds within the ossified deposits rather than at the interface between hard and soft tissues. Our approach could effectively capture the microstructural changes occurring during loading and shows promise in understanding the relation between microstructure and mechanical response for ex-vivo Achilles tendons and other biological tissues.