Weakness affects motor performance and causes skeletal deformities in spinal muscular atrophy (SMA). Scoliosis surgery decision-making is based on curve progression, pulmonary function, and skeletal maturity. Benefits include quality of life, sitting balance, and endurance. Post-operative functional decline has not been formally assessed.To assess the impact of scoliosis surgery on motor function in SMA types 2 and 3.Prospective data were acquired during a multicenter natural history study. Seventeen participants (12 type 2, 5 type 3 with 4 of the 5 having lost the ability to ambulate) had motor function assessed using the Hammersmith Functional Motor Scale Expanded (HFMSE) performed pre-operatively and at least 3 months post-operatively. Independent t-tests determined group differences based on post-operative HFMSE changes, age, and baseline HFMSE scores.Three participants had minimal HFMSE changes (±2 points) representing stability (mean change = -0.7). Fourteen participants lost >3 points, representing a clinically meaningful progressive change (mean change = -12.1, SD = 8.9). No participant improved >2 points. There were no age differences between stable and progressive groups (p = 0.278), but there were significant differences between baseline HFMSE (p = 0.006) and change scores (p = 0.001). Post-operative changes were permanent over time.Scoliosis surgery has an immediate impact on function. Baseline HFMSE scores anticipate post-operative loss as higher motor function scores were associated with worse decline. Instrumentation that includes fixation to the pelvis reduces flexibility, limiting the ability for compensatory maneuvers. These observations provide information to alert clinicians regarding surgical risk and to counsel families.