The morphological characteristics of skeletal muscles innervated caudal to a spinal cord injury (SCI) undergo dramatic phenotypic and microvascular changes, which vary with location and degree of trauma. Here we utilise a severe contusion model of SCI in adult female Sprague Dawley rats. A total of 20 animals were used in this study, 16 of which received a 250 kdyn contusion to the mid-line of the spinal cord at T9/10, while four remained intact (CT) and were used to compare the level of recovery among the SCI and training groups. Following spinal cord injury, animals were randomly assigned to one of four groups, locomotor training (TR), epidural stimulation (ES) or a combination of the two (CB). Cage control (CGCT) animals received the contusion and were left for the duration of the study untrained. Muscle fibre phenotype and local capillary supply area were determined for the tibialis anterior muscle (TA) across two distinct compartments within the muscle, the oxidative core and the glycolytic cortex. SCI induced a significant shift in Type II fibre phenotype from oxidative (IIa) to glycolytic (IIx/b) (P<0.05), as well as rarefaction of the capillary bed within both the oxidative core and glycolytic cortex, compared to intact weight matched controls (decreased C:F and CD, P<0.05). Microvascular pruning reduced capillary spatial heterogeneity, while increasing mean supply (domain) area, with a normalising of local capillary supply per fibre area (LCD) across the three main fibre types. ES and TR showed no angiogenic response across the TA, while their capillary rarefaction and hypertrophic remodelling further reduced local capillary supply to glycolytic fibres, further decreasing oxygen supply capacity of the muscle. Conversely, CB treatment increased C:F in the core and cortex, by 31% and 18%, respectively (CB vs. CGCT, P<0.05). The angiogenic response improved capillary homogeneity in the core and cortex, while decreasing the mean capillary domain area in both compartments. This suggests targetted angiogenesis around glycolytic fibres, as local capillary to fibre ratio (LCFR) increased significantly for Type IIa and IIx/b fibres, compared to CGCT animals. There appears to be an important role for weight bearing locomotor training in maintaining oxidative fibre composition, and in combination with ES there is improved maintenance of glycolytic capillary supply area than in standalone treatments.