With the recent and ongoing sample return missions and/or the developments of nano-to microscale 3-D and 2-D analytical techniques, it is necessary to develop sample preparation and analysis protocols that allow combination of different nanometer-to micrometer-scale resolution techniques and both maximize scientific outcome and minimize sample loss and contamination. Here, we present novel sample preparation and analytical procedures to extract a maximum of submicrometer structural, mineralogical, chemical, molecular, and isotopic information from micrometric heterogeneous samples. The sample protocol goes from a nondestructive infrared (IR) tomography of~10 to~70 µm-sized single grains, which provides the distribution and qualitative abundances of both mineral and organic phases, followed by its cutting in several slices at selected sites of interest for 2-D mineralogical analysis (e.g., transmission electron microscopy), molecular organic and mineral analysis (e.g., Raman and/or IR microspectroscopy), and isotopic/chemical analysis (e.g., NanoSIMS). We also discuss here the importance of the focused ion beam microscopy in the protocol, the problems of sample loss and contamination, and at last the possibility of combining successive different analyses in various orders on the same micrometric sample. Special care was notably taken to establish a protocol allowing correlated NanoSIMS/TEM/IR analyses with NanoSIMS performed first. Finally, we emphasize the interest of 3-D and 2-D IR analyses in studying the organics-minerals relationship in combination with more classical isotopic and mineralogical grain characterizations.