This study investigated whether exercise-induced muscle damage (EIMD) resulted in changes to whole-body substrate utilisation during exercise performed during the subsequent 48 hours. Eight males (31 ± 6 years) performed 30 minutes of bench-stepping exercise. One leg performed eccentric contractions (Ecc) by lowering the body whilst the control leg performed concentric contractions (Con) by raising the body. On the two days following bench-stepping exercise participants performed measures of muscle function on an isokinetic dynamometer and undertook a bout of one leg cycling exercise, at two differing workloads, with the first workload (WL1) at 1.5 ± 0.25 W/kg and the second workload (WL2) at 1.8 ± 0.25 W/kg with each leg. Expired respiratory gases were collected during cycling to estimate whole body substrate utilisation. There were significant decrements in measures of muscular performance (isometric force, concentric and eccentric torque) and increased perception of soreness in Ecc compared with Con (P < 0.05). The effect of the Ecc treatment on substrate utilisation during one-legged cycling revealed a significant trial × time interaction with higher rates of CHO oxidation in the Ecc condition compared with Con that were further increased 48 hours later (P = 0.02). A significant treatment × time × effort interaction (P < 0.01) indicated the effect of the treatment altered as workload increased with higher rates of CHO oxidation occurring in WL2. This is consistent with greater reliance upon muscle glycogen. Suggesting that in EIMD, reductions in strength and increased feelings of soreness can be associated with greater reliance upon intramuscular CHO oxidation, than lipid, during subsequent concentric work.