In this paper, an integrated and automated methodology for the coupling between 1D- and 3D-CFD simulation codes is presented, which has been developed to support the design and calibration of new diesel engines. The aim of the proposed methodology is to couple 1D engine models, which may be available in the early stage engine development phases, with 3D predictive combustion simulations, in order to obtain reliable estimates of engine performance and emissions for newly designed automotive diesel engines. The coupling procedure features simulations performed in 1D-CFD by means of GT-SUITE and in 3D-CFD by means of Converge, executed within a specifically designed calculation methodology. An assessment of the coupling procedure has been performed by comparing its results with experimental data acquired on an automotive diesel engine, considering different working points, including both part load and full load conditions. Different multiple injection schedules have been evaluated for part-load operation, including pre and post injections. The proposed methodology, featuring detailed 3D chemistry modeling, was proven to be capable assessing pollutant formation properly, specifically to estimate NOx concentrations. Soot formation trends were also well-matched for most of the explored working points. The proposed procedure can therefore be considered as a suitable methodology to support the design and calibration of new diesel engines, due to its ability to provide reliable engine performance and emissions estimations from the early stage of a new engine development.