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CO2 emissions originating from the construction industry have a significant impact on global warming where the production of ordinary Portland cement clinker is responsible for similar to 8% of all human-made CO2. Alkali-doped calcium silicate hydrate (C-S-H) is a critical silicate material in industry since the use of blended cements and alkali-activated materials in construction can substantially reduce human-made CO2 emissions. However, the effect of alkali doping (Na and K) on the long-term stability and associated durability of C-S-H remains an open question. Here, using first-principles quantum chemistry calculations on the model crystalline phase clinotobermorite, we show that there is a strong interplay between the thermodynamic stability of alkali-doped C-S-H and the symmetry of the alkali atoms in the structure. Our results reveal that a symmetrical distribution of alkali atoms leads to a higher stability value such that stable structures with moderate alkali concentrations can be obtained provided that the alkali atoms are allowed to settle into a symmetrical distribution. We show the associated structural mechanisms of this stability by calculating the migration barriers of alkali atoms within the material, the electronic charge distribution in the material, and the variation of basal spacing by using both computational methods and X-ray diffraction analysis.