Alkali-activated materials and related alternative cementitious systems are sustainable technologies that have the potential to substantially lower the CO2 emissions associated with the construction industry. However, these systems have augmented chemical compositions as compared to ordinary Portland cement (OPC), which may impact the evolution of the hydrate phases. In particular, calcium-silicate-hydrate (C–S–H) gel, the main hydrate phase in OPC, is likely to be altered at the atomic scale due to changes in the bulk chemical composition, specifically via the addition of alkalis (i.e., Na or K) and aluminum. Here, via density functional theory calculations, we reveal the presence of a charge balancing mechanism at the molecular level in C–S–H gel (as modeled using crystalline 14 Å tobermorite) when alkalis and aluminum atoms are introduced into the structure. Different structural representations are obtained depending on the level of substitution and the degree of charge balancing incorporated in the structures. The impact of these substitutional and charge balancing effects on the structures is assessed by analyzing the formation energies, local bonding environments, diffusion barriers and mechanical properties. The results of this computational study provide information on the phase stability of alkali/aluminum containing C–S–H gels, shedding light on the fundamental atomic level mechanisms that play a crucial role in these complex disordered materials.