The organic–inorganic nature of organic-rich source rocks poses several challenges for the development of functional relations that link mechanical properties with geochemical composition. With this focus in mind, we herein propose a method that enables chemo-mechanical characterization of this highly heterogeneous source rock at the micron and submicron length scale through a statistical analysis of a large array of energy-dispersive X-ray spectroscopy (EDX) data coupled with nanoindentation data. The ability to include elemental composition to the indentation probe via EDX is shown to provide a means to identify pure material phases, mixture phases, and interfaces between different phases. Employed over a large array, the statistical clustering of this set of chemo-mechanical data provides access to the properties of the fundamental building blocks of clay-dominated organic-rich source rocks. The versatility of the approach is illustrated through the application to a large number of source rocks of different origin, chemical composition, and organic content. We find that the identified properties exhibit a unique scaling relation between stiffness and hardness. This suggests that organic-rich shale properties can be reduced to their elementary constituents, with several implications for the development of predictive functional relations between chemical composition and mechanical properties of organic-rich source rocks such as the intimate interplay between clay-packing, organic maturity, and mechanical properties of porous clay/organic phase.