People with spinal cord injury (SCI) tend to be more sedentary and increase fat accumulation, which could have a negative influence on metabolic flexibility. The aim of this study was to investigate the capacity to oxidize fat in a homogenous sample of men with thoracic SCI compared with healthy noninjured men during an arm cycling incremental test. Forty-one men, 21 with SCI and 20 noninjured controls, performed an incremental arm cycling test to determine peak fat oxidation (PFO) and the intensity of exercise that elicits PFO (Fat_max). PFO was expressed in absolute values (g/min) and relative to whole-body and upper-body lean mass ([mg·min⁻¹]·kg⁻¹) through three different models (adjusting by cardiorespiratory fitness and fat mass). Gross mechanical efficiency was also calculated. PFO was higher in SCI than in noninjured men (0.27 ± 0.07 vs. 0.17 ± 0.07 g/min; 5.39 ± 1.30 vs. 3.29 ± 1.31 [mg·min⁻¹]·kg⁻¹ whole-body lean mass; 8.28 ± 2.11 vs. 5.08 ± 2.12 [mg·min⁻¹]·kg⁻¹ upper-body lean mass). Fat_max was found at a significantly higher percentage of VO₂peak in men with SCI (33.6% ± 8.2% vs. 23.6% ± 6.4%). Differences persisted and even increased in the fully adjustment model and at any intensity. Men with SCI showed significantly higher gross mechanical efficiency at 35 and 65 W than the noninjured group. Men with SCI showed higher fat oxidation when compared with noninjured men at any intensity, even increased after full adjustment for lean mass, fat mass, and cardiorespiratory fitness. These findings suggest that SCI men could improve their metabolic flexibility and muscle mass for greater efficiency, not being affected by their fat accumulation.