In order to design structures with sufficient safety, it is necessary to consider uncertainties resulting from simplified modelling approaches or unknown scatter of physical parameters. These uncertainties are incorporated into design equations by the application of partial safety factors. While these uncertainties are dependent on the structural models, their influence of the choice of model on the partial safety factors is currently not taken into account. Despite the existence of proposed values for the uncertainty in calculation of action and resistance side for steel or concrete structures, these are limited in case of steel-concrete composite structures. This paper derives therefore model uncertainties for cross-sectional resistance checks for steel-concrete composite bridges in the sagging and hogging region. Rather than investigating the model-dependent uncertainties on the action and resistance side independently, an approach is adopted which combines both sides. A geometrical and material non-linear finite element model of a bridge girder has been developed and validated against experimental results in order to investigate the prediction of action and resistance according to simplified models. In order to evaluate the failure of the structure, this paper discusses different approaches to determining the failure point of the finite element model. Besides quantifying the conservatism in the current design of composite bridge cross-sections, this paper also determines uncertainties with respect to the scatter of the input parameters by performing Monte Carlo simulations. These results can then further be used to derive partial safety factors considering model-dependent uncertainties.