Scapular kinematic estimates are altered by soft tissue artefacts, therefore experimental and numerical methods should be developed to improve their accuracy. This study aimed to assess the influence of weights applied to the scapula markers within a closed-loop multibody kinematic optimization on scapular kinematic estimates. Fifteen healthy volunteers performed static postures mimicking analytical, daily living and sport movements. Scapulo-thoracic angles were computed either from a scapula locator as the reference, or from a closed-loop multibody-kinematic optimization (MKO) including a participant-specific point-on-ellipsoid scapulothoracic joint. Weights applied to scapula markers in the MKO were optimized to minimize the difference in scapular orientation from the reference. Optimizing weighting sets significantly (p < 0.0001) improved scapular orientation from 0.9° to 12.1° in comparison to scapular kinematics estimated with non-optimized weighting sets. The mean optimized weighting set contained no neglectable weight for all markers from the acromion to the medial border of the scapular spine but showed no significant difference (p = 0.547) compared to homogeneous weights. Optimized weighting sets were participant- and movement- specific. To conclude, homogenous weights applied on redundant markers located from acromion to scapular medial border spine are recommended when estimating scapular kinematics in upper limb MKO.