Spinal muscular atrophy (SMA) is a recessive genetic disorder marked by a deficiency in SMN2 protein, primarily affecting lower motor neurons and the neuromuscular junction, leading to muscle weakness and fatigue. While neuronal and neuromuscular pathology are central to SMA symptoms, emerging evidence indicates significant non-neuronal tissue changes. Recent disease-modifying therapies targeting the central nervous system can enhance SMN2 production and mitigate clinical severity; however, persistent weakness and fatigue suggest underlying muscle pathology that these treatments do not address. Animal models of SMA have revealed mitochondrial dysfunction and impaired biogenesis. Near-infrared spectroscopy (NIRS) is a non-invasive technique that allows for real-time assessment of local oxygen metabolism in skeletal muscle in vivo. Previous NIRS studies in SMA have demonstrated decreased oxygen consumption and increased fatigue, aligning with findings from cardiopulmonary exercise testing (CPET). NIRS can provide insights into muscle tissue characteristics and potential therapeutic targets. In this study, we evaluated 45 participants (8 controls and 37 with SMA) during the assisted six-minute cycle test (A6MCT). Each participant engaged in a 6-minute upper extremity exercise followed by a 5-minute recovery period, wearing two portable SRS NIRS devices (Artinis, PortaLite) on the bicep and triceps. These devices measured relative changes in deoxyhemoglobin (ΔHHb) and oxyhemoglobin (ΔO2Hb) at 10 Hz during both periods. The data were used to calculate the tissue saturation index (TSI), a semi-quantitative measure reflecting real-time muscle oxygen saturation, which correlates closely with the minute rate of oxygen consumption (VO2m). Group-level comparisons revealed that SMA participants exhibited significantly higher minimum oxygen saturation (61.54 ± 5.56) and a reduced slope (-9.35 ± 5.54) during exercise compared to controls (58.67 ± 5.53 and -11.65 ± 3.56). During recovery, SMA patients showed a lower maximum TSI (78.1 ± 3.21) and a slower recovery rate (15.41 ± 3.56) compared to controls (82.24 ± 5.58 and 21.3 ± 3.2). This study confirms reduced skeletal muscle function and oxidative capacity in SMA during exercise, consistent with prior research. The diminished magnitude and slower recovery rate observed in SMA patients suggest primary muscle pathology, potentially linked to mitochondrial dysfunction. Further investigation, in conjunction with CPET and electromyography (EMG), is essential to elucidate the impact on skeletal muscle function and identify mechanisms that could inform more effective treatments.