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Cement hydration has a direct influence on the mechanical and durability properties of concrete. Understanding the formation and evolution of hydration products at atomic scale during different stages of hydration is important in order to engineer the material for specific performance. However, research investigations on the effects of adding supplementary materials like fly ash (FA) on the development of the atomic scale structure of the major hydration product, calcium silicate hydrate (C–S–H), and its correlations with nanomechanical properties (through complementary physicochemical and nanomechanical techniques) are scanty. In this work, FA was added to Portland cement in different percentages (20% and 40%) to study its effect on the structural and mechanical properties at different phases of hydration (3–90 days). The evolution of C–S–H at atomic scale in cement–FA systems was studied using X-ray diffraction, atomic pair distribution function, high-resolution transmission electron microscopy, field emission scanning electron microscopy and Fourier-transform infrared spectroscopy, and mechanical properties at different ages were evaluated using a nanoindentation technique. The information and critical observations from this study provide significant information on intrinsic properties of hydrating cement composites, which will help in developing low-energy cement composites for sustainable structures. [ABSTRACT FROM AUTHOR]