Subject-specific scaling of cadaver-based musculoskeletal models is important for accurate musculoskeletal analysis within multiple areas such as ergonomics, orthopaedics and occupational health. We present two procedures to scale ‘generic’ musculoskeletal models to match segment lengths and joint parameters to a specific subject and compare the results to a simpler approach based on linear, segment-wise scaling. By incorporating data from functional and standing reference trials, the new scaling approaches reduce the model sensitivity to assumed model marker positions. For validation, we applied all three scaling methods to an inverse dynamics-based musculoskeletal model and compared predicted knee joint contact forces to those measured with an instrumented prosthesis during gait. Additionally, a Monte Carlo study was used to investigate the sensitivity of the knee joint contact force to random adjustments of the assumed model marker positions (+/− one marker diameter). The model based on linear scaling showed the highest variation in the knee joint contact force of 1.44 body weight (BW) around contra-lateral heel strike, and a variation in root mean square deviation (RMSD) of 0.36 BW. The proposed methods reduced the variation to 1.0 BW (RMSD 0.26 BW) for the anatomical landmark based method and 0.47 BW (RMSD 0.06 BW) for the functional based method. Variation in model predictions due to uncertainty in marker positions is a trait of all marker-based musculoskeletal modelling approaches. The presented methods solve part of this problem and rely less on manual identification of anatomical landmarks in the model. The work represents a step towards a more consistent methodology in musculoskeletal modelling.