Geopolymers are low-calcium, sustainable cementitious materials. The role of Zn, a known retardant used in Portland cement, in geopolymer systems is not well understood. This study scrutinises the effect of Zn on metakaolin-based geopolymer reaction mechanisms and kinetics, and investigates the incorporation mechanism of Zn in geopolymer gels. Isothermal calorimetry and X-ray diffraction analyses show that substitution of ZnO (20 mol% c.f. metakaolin) significantly hinders reaction, likely due to preferential formation of a Na/K-Zn containing phase. Solid-state nuclear magnetic resonance spectroscopy shows that Zn²⁺ partially substitutes for Na⁺/K⁺ in charge-balancing sites within the geopolymer gel. Setting time and leaching tests show that the retarding effect of Zn on reaction kinetics is significantly greater in Na-activated geopolymers compared with K-activated geopolymers, whereas Na-activated geopolymers exhibit superior fixation capacity to Zn. A lab-scale experiment demonstrates that metakaolin-based geopolymers are promising candidates for the stabilisation/solidification of Zn-rich hazardous waste.