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This paper summarizes recent developments in the field of nanoindentation analysis of highly heterogeneous composites. The fundamental idea of the proposed approach is that it is possible to assess nanostructure from the implementation of micromechanics-based scaling relations for a large array of nanoindentation tests on heterogeneous materials. We illustrate this approach through the application to Calcium-Silicate-Hydrate (C-S-H), the binding phase of all cement-based materials. For this important class of materials we show that C-S-H exists in at least three structurally distinct but compositionally similar forms: Low Density (LD), High Density (HD) and Ultra-High-Density (UHD). These three forms differ merely in the packing density of five nano-meter sized particles. The proposed approach also gives access to the solid particle properties of C-S-H, which can now be compared with results from atomistic simulations. By way of conclusion, we show how this approach provides a new way of analyzing complex hydrated nanocomposites, in addition to classical microscopy techniques and chemical analysis. This approach will turn out invaluable in our quest of adding the necessary “green” value to a commodity, concrete, by nano-engineering higher strength and toughness from first principles.