While ensuring the long-term integrity of wellbore sealants is critical for the success of geological carbon storage (GCS), the chemical degradation of conventional materials under CO₂-rich conditions remains a major challenge. This study investigates the carbonation behavior of a one-part granite-based geopolymer, integrating a novel pore-scale simulation framework with experimental validation. A new model, ReacSan, is developed to simulate CO₂ transport and carbonation reactions within the evolving microstructure of the geopolymer under GCS-relevant conditions. The framework incorporates CO₂ dissolution using the Redlich–Kwong equation of state, gel dissolution via transition state theory, ion transport using the Lattice Boltzmann Method, and chemical reactions through thermodynamic modeling. The model was validated through experiments exposing equivalent geopolymer samples to CO₂ under in-situ conditions. The experimentally observed rapid carbonation, leading to a decrease in pore fluid pH and the precipitation of CaCO₃ matched the numerical simulations well, demonstrating the ability of the novel ReacSan framework to capture both temporal and spatial variations in the microstructure and carbonation mechanisms of alkali-activated materials (AAMs) exposed to supercritical CO₂. Based on the demonstrated validity of the model, the model is capable of providing detailed predictions of carbonation progression of AAMs or any other sealants over longer time- and length-scales required to ensure long-term GCS integrity.