The Earth's crust is exceptionally important to understand the geological evolution of our planet and to access natural resources as minerals, critical raw materials, geothermal energy, water, hydrocarbons, etc.. However, in many regions of the world it is still poorly modelled and understood. Here we present the latest advance on three-dimensional modelling of the Mediterranean Sea crust based on freely available global gravity and magnetic field models. The proposed model, based on the inversion of gravity and magnetic field anomalies constrained by available a-priori information (such as interpreted seismic profiles, previous studies, etc.), provides, with an unprecedented spatial resolution of 15 km, the depths of the main modelled geological horizons (Plio-Quaternary, Messinian and Pre-Messinian sediments, crystalline crust and upper mantle), coherent with the known available constraints, together with the three-dimensional distribution of density and magnetic susceptibility. The inversion is carried out by means of a Bayesian algorithm, which allows to modify at the same time the geometries and the three dimensional distributions of density and magnetic susceptibility, always respecting the constraints introduced by the initial information. In addition to unveil the structure of the crust beneath the Mediterranean Sea, the present study also shows the informative content of freely available global gravity and magnetic models, thus putting the base for the development of future high resolution models of the Earth crust at global level.Correction available here : https://doi.org/10.1038/s41598-023-37289-5