Immediate two-stage subpectoral implant breast reconstruction after mastectomy requires the surgical disinsertion of the sternocostal fiber region of the pectoralis major (PM). The disinsertion of the PM would need increased contributions from intact shoulder musculature to generate shoulder torques. This study aimed to identify neuromuscular compensation strategies adopted by subpectoral implant breast reconstruction patients using novel muscle synergy analyses. Fourteen patients treated bilaterally with subpectoral implant breast reconstruction (>2.5 years post-reconstruction) were compared to ten healthy controls. Surface electromyography was obtained from sixteen shoulder muscles as participants generated eight three-dimensional (3D) shoulder torques in five two-dimensional arm postures bilaterally. Non-negative matrix factorization revealed the muscle synergies utilized by each experimental group on the dominant and non-dominant limbs, and the normalized similarity index assessed group differences in overall synergy structure. Bilateral subpectoral implant patients exhibited similar shoulder strength to healthy controls on the dominant and non-dominant arms. Our results suggest that 3D shoulder torque is driven by three shoulder muscle synergies in both healthy participants and subpectoral implant patients. Two out of three synergies were more similar than is expected by chance between the groups on the non-dominant arm, whereas only one synergy is more similar than is expected by chance on the dominant arm. While bilateral shoulder strength is maintained following bilateral subpectoral implant breast reconstruction, a closer analysis of the muscle synergy patterns underlying 3D shoulder torque generation reveals that subpectoral implant patients adopt compensatory neuromuscular strategies only with the dominant arm.