Simulation‐based digital twins must provide accurate, robust, and reliable digital representations of their physical counterparts. Therefore, quantifying the uncertainty in their predictions plays a key role in making better‐informed decisions that impact the actual system. The update of the simulation model based on data must then be carefully implemented. When applied to complex structures such as bridges, discrepancies between the computational model and the real system appear as model bias, which hinders the trustworthiness of the digital twin and increases its uncertainty. Classical Bayesian updating approaches aimed at inferring the model parameters often fail to compensate for such model bias, leading to overconfident and unreliable predictions. In this paper, two alternative model bias identification approaches are evaluated in the context of their applicability to digital twins of bridges. A modularized version of Kennedy and O'Hagan's approach and another one based on Orthogonal Gaussian Processes are compared with the classical Bayesian inference framework in a set of representative benchmarks. Additionally, two novel extensions are proposed for these models: the inclusion of noise‐aware kernels and the introduction of additional variables not present in the computational model through the bias term. The integration of these approaches into the digital twin corrects the predictions, quantifies their uncertainty, estimates noise from unknown physical sources of error, and provides further insight into the system by including additional pre‐existing information without modifying the computational model.