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Modern diesel engines are typically equipped with common rail injection system, variable geometry turbocharger and exhaust gas recirculation system in order to meet the emissions standards. While the electronic fuel control has been extensively developed and used in the common rail injection systems, the “in-air cylinders filling” control remains poorly exploited. In this paper, we suggest a dynamic engine optimization process that predicts, under transient conditions, the optimal values of the intake pressure and the compressor mass flow rate to be applied to the engine based on pollution criteria such as the opacity. The optimization procedure and a physical mean value model describing the functioning of a variable geometry turbocharged diesel engine and its smoke's opacity are shown in details. The simulations results of the engine's model are in excellent agreement with the experimental data collected on test bench.