The durability of concrete structures can be compromised by alkali-aggregate reaction, a chemical process between the alkalis and reactive minerals within the aggregate. The reaction produces a gel of hydrated sodium-potassium-calcium silicate that expands in the concrete, deteriorating it. Adding mineral admixtures to concrete is recognized as a highly effective strategy to mitigate expansion due to alkali-aggregate reactions. This study investigated the use of a natural mineral admixture, metahalloysite, to mitigate the reaction effects. Expansion tests were conducted according to ASTM C441. The microstructure of the expanded specimens was examined using computed tomography and scanning electron microscopy coupled with X-ray microanalysis. The results showed that the 25% cement substitution with metahalloysite significantly lowered the swelling of the concrete specimens, keeping it within safe limits. Microstructural examination of the specimens without admixture showed numerous cracks in the aggregate grains, the presence of reaction products, and ettringite crystals. Specimens with admixture showed the presence of non-swelling sodium-potassium silicate gel and a dense C-S-H phase with a reduced C/S ratio.