This paper considers a model based turbocharger control strategy for a Diesel engine fitted with a variable geometry turbocharger and two EGR circuits. Compared with controllers based on lookup tables, the model based control law is very successful specially that it adapts with the physical behavior of the system studied. Is this paper we propose to affine this strategy and make it more robust, specially for modeling errors and sensors fault, to ensure an accurate regulation for the intake manifold pressure. Therefore, we observe that the turbine efficiency, which is used in the model based control law, is a key variable for this purpose. Thus, the main contribution of this paper is to combine the model based controller with an estimator of the turbine efficiency. By adapting online the efficiency map, all the modeling errors in the control law will be significantly reduced, particularly at steady state with benefits also provided during transients. This strategy decrease also the impact of different sensors fault, used to feed the controller, and can be used for fault detection application. The proposed method is validated using both engine simulations and experimental tests.