Background Shoulder biomechanics and spine alignment have been found to be related to occasional and/or chronic neck–shoulder pain. Pilates is a physical training approach that focuses on posture, flexibility, segmental alignment and core control, through posture and movement exercises. The objectives of this study were to determine the effect of a Pilates training program on arm–trunk posture, strength, flexibility and biomechanical patterns during a functional shoulder flexion task. Methods Nineteen subjects (9 controls, 10 experimental) were assessed twice, 12 weeks apart, during which the experimental group was submitted to a Pilates training program (two 1-h sessions per week). The assessment consisted of trials of seated posture, abdominal strength, shoulder range of motion, and maximal shoulder flexion, during which neck, shoulder and trunk kinematics and the activity of 16 muscles were recorded. Findings After training, subjects showed smaller static thoracic kyphosis during quiet sitting and greater abdominal strength. The experimental group also showed reduced posterior and mediolateral scapular displacements, upper thoracic extension and lumbar lateral flexion, as well as higher activity of the ipsilateral cervical erector spinae, contralateral rhomboid muscles and lower activity of the ipsilateral lumbar erector spinae during the shoulder flexion task. Interpretation The Pilates training program was effective in improving abdominal strength and upper spine posture as well as in stabilizing core posture as shoulder flexion movements were performed. Since deficits in these functional aspects have previously been associated with symptoms in the neck–shoulder region, our results support the use of Pilates in the prevention of neck–shoulder disorders.