Numerous geosciences samples display a multi-scale mineralogical heterogeneity for which it is challenging to obtain spatially resolved quantitative chemical data. It is the case for chondritic meteorites, which can contain up to 10 different phases with grain size ranging from the nanometer to the millimeter. We developed a method providing multiple physical and chemical information by advanced scanning electron microscopy (SEM), hyperspectral energy dispersive X-ray spectroscopy (EDX) and electron probe micro-analyses (EPMA). The method includes: i) infra-micrometric low-voltage EDX mapping and innovative post-acquisition hyperspectral data analysis (based on both clustering and multiple linear least square fitting) which allow phase mapping and quantification of the modal abundances; ii) EPMA of chemical end-members to upgrade the phase map into a quantified chemical map; iii) physical modeling of the EDX background, used as a proxy of the density. Density maps can be obtained with a precision of ~10%; iv) determination of the bulk sample composition by combining modal abundances, chemical analysis and density measurements.The approach is applied to three well-known chondrites (Murchison, Paris and Orgueil), showing heterogeneous grain sizes and mineralogy. Areas of ~250 ∗ 250 μm2 were mapped with a pixel size of 250 nm to determine the modal abundances, size distribution, circularity and densities of all phases, as well as the matrix bulk compositions. Taking bulk wet chemistry data as reference, ACADEMY leads to a better match than published defocused beam EPMA measurements. We demonstrate that choosing a Fe-rich, hydrated standard (a biotite) to quantify phyllosilicate by EPMA improves the quantification by up to 10%, and we ultimately retrieve the Mg/Si ratio with a 1% precision. We called this method ACADEMY for Analyzing the Composition, the modal Abundance and the Density using Electron MicroscopY. A code was developed and was made available online so that ACADEMY can be applied to other materials.