The estimation of muscle forces in musculoskeletal shoulder models is still controversial. Two different methods are widely used to solve the indeterminacy of the system: electromyography (EMG)-based methods and stress-based methods. The goal of this work was to evaluate the influence of these two methods on the prediction of muscle forces, glenohumeral load and joint stability after total shoulder arthroplasty. An EMG-based and a stress-based method were implemented into the same musculoskeletal shoulder model. The model replicated the glenohumeral joint after total shoulder arthroplasty. It contained the scapula, the humerus, the joint prosthesis, the rotator cuff muscles supraspinatus, subscapularis and infraspinatus and the middle, anterior and posterior deltoid muscles. A movement of abduction was simulated in the plane of the scapula. The EMG-based method replicated muscular activity of experimentally measured EMG. The stress-based method minimised a cost function based on muscle stresses. We compared muscle forces, joint reaction force, articular contact pressure and translation of the humeral head. The stress-based method predicted a lower force of the rotator cuff muscles. This was partly counter-balanced by a higher force of the middle part of the deltoid muscle. As a consequence, the stress-based method predicted a lower joint load (16% reduced) and a higher superior-inferior translation of the humeral head (increased by 1.2 mm). The EMG-based method has the advantage of replicating the observed cocontraction of stabilising muscles of the rotator cuff. This method is, however, limited to available EMG measurements. The stress-based method has thus an advantage of flexibility, but may overestimate glenohumeral subluxation.