Ultra-high-performance cement-based materials produced under different conditions have been characterized by transmission electron microscopy (TEM), scanning transmission electron Microscopy (STEM), high resolution transmission microscopy (HRTM) and chemical analysis. In addition to cement, these materials contain large amounts of crushed quartz and amorphous submicrometre silica. A post-set heat treatment was also applied in some cases. An abrasive thinning method combined with grazing angle ion etching allowed the preparation of 100 nm thick specimens with wide observation surface areas while avoiding any water or CO2 contact which may cause changes. Clinker, silica fume and crushed quartz reactivity as a function of the curing processes have been studied, as well as the interfacial zones with the hydrated matrices. The Ca/Si ratio spatial distribution in hydrated products has been analyzed and shown to undergo strong local fluctuations. Nevertheless, the composition fluctuations were less pronounced and the average Ca/Si ratio was lower than in silica-free cement paste. HRTM lattice imaging shows the coexistence of nanocrystalline phases and mesoscale ordered regions within an amorphous matrix. A d-spacings analysis of the nanocrystalline phase suggests a tobermorite-like structure for the calcium silicate hydrates, whereas the mesoscale order might reflect modulations in the water content.