Establishing the links between the composition, microstructure and mechanics of shale continues to be a formidable challenge for the geomechanics community. In this study, a robust methodology is implemented to access the in situ chemomechanics of this sedimentary rock at micrometer length scales. Massive grids of coupled wave dispersive spectroscopy (WDS) and instrumented indentation experiments were performed over representative material surfaces to accommodate the highly heterogeneous composition and microstructure of shale. The extensive datasets of compositional and mechanical properties were analyzed using multi-variate clustering statistics to determine the attributes of active phases present in shale at microscales. Our chemomechanical analysis confirmed that the porous clay (PC) mechanical phase inferred by statistical indentation corresponds to the clay mineral phase defined strictly on chemical grounds. The characteristic stiffness and hardness behaviors of the PC are realized spatially in regions removed from silt inclusions of quartz and feldspar. At the microscale shared by indentation and WDS experiments, a consistent chemomechanical signature for shale emerges in which the heterogeneities of the PC are captured by the standard deviations of indentation properties and concentrations of chemical elements. However, these local behaviors are of second order compared to the global trend observed for mean mechanical properties and the clay packing density, which synthesizes the relative volumes of clay and nanoporosity in the material. The coupled statistical indentation and WDS technique represents a viable approach to characterize the chemomechanics of shale and other natural porous composites at a consistent scale below the macroscopic level.