Early diagnosis of deep tissue injury remains problematic due to the complicated and multi-factorial nature of damage induction, and the many processes involved in damage development and recovery. In this paper we present a comprehensive assessment of deep tissue injury development and remodeling in a rat model by multi-parametric magnetic resonance imaging (MRI) and histopathology. The tibialis anterior muscle of rats was subjected to mechanical deformation for 2 h. Multi-parametric in vivo MRI, consisting of T2, T2∗, mean diffusivity (MD), and angiography measurements, was applied before, during, and directly after indentation, as well as at several time points during a 14 days follow-up. MRI readouts were linked to histological analyses of the damaged tissue. The results showed dynamic change in various MRI parameters, reflecting the histopathological status of the tissue during damage induction and repair. Increased T2corresponded with edema, muscle cell damage, and inflammation. T2∗ was related to tissue perfusion, hemorrhage, and inflammation. MD increase and decrease reported on the tissue's microstructural integrity and reflected muscle degeneration, edema, as well as fibrosis. Angiography provided information on blockage of blood flow during deformation. Our results indicate that the effects of a single damage causing event of only 2 h deformation were present up to 14 days. The initial tissue response to deformation, as observed by MRI, starts at the edge of the indentation. The quantitative MRI readouts provided distinct and complementary information on the extent, temporal evolution, and microstructural basis of deep tissue injury related muscle damage.