Gelation and densification of calcium–silicate–hydrate take place during cement hydration. Both processes are crucial for the development of cement strength, and for the long-term evolution of concrete structures. However, the physicochemical environment evolves during cement formation, making it difficult to disentangle what factors are crucial for the mechanical properties. Here we use Monte Carlo and Molecular Dynamics simulations to study a coarse-grained model of cement formation, and investigate the equilibrium and arrested states. We can correlate the various structures with the time evolution of the interactions between the nano-hydrates during the preparation of cement. The novel emerging picture is that the changes of the physicochemical environment, which dictate the evolution of the effective interactions, specifically favour the early gel formation and its continuous densification. Our observations help us understand how cement attains its unique strength and may help in the rational design of the properties of cement and related materials.