The numerical model HydratiCA was used to simulate the reaction kinetics of alkali-activated metakaolin, a material belonging to a class of sustainable binders alternative to Portland cement. The full chemistry of the system, including solid phases and aqueous species, is taken into account in these simulations. Specifically, metakaolin dissolution, reaction product nucleation and growth, and ion speciation, and diffusion in solution are simulated. The sodium aluminosilicate (N-A-S-H), formed by the reaction of metakaolin in alkaline solution, is implemented in the model as a combination of co-precipitating pseudo-zeolitic phases, with variable stoichiometry. The results show how variations of the reaction pathways, occurring when alkaline activators of different composition and concentration are used, can be associated with different macroscopic behaviors in terms of mechanical performance and durability. Reconciling these macroscopic properties with the basic chemical processes will be a fundamental technological challenge for the deployment of sustainable technologies in the construction industry.