The encapsulation of caesium (Cs) and strontium (Sr) contaminated clinoptilolite in Na and K based metakaolin geopolymers is reported. When Cs or Sr loaded clinoptilolite is mixed with a metakaolin geopolymer paste, the high pH of the activating solution and the high concentration of ions in solution cause ion exchange reactions and dissolution of clinoptilolite with release of Cs and Sr into the geopolymer matrix. The leaching of Cs and Sr from metakaolin-based geopolymer has therefore been investigated. It was found that Na-based geopolymers reduce leaching of Cs compared to K-based geopolymers and the results are in agreement with the hard and soft acids and bases (HSAB) theory. Cs ions are weak Lewis acids and aluminates are a weak Lewis base. During the formation of the geopolymer matrix Cs ions are preferentially bound to aluminate phases and replace Na in the geopolymer structure. Sr uptake by Na-geopolymers is limited to 0.4 mol Sr per mole of Al and any additional Sr is immobilised by the high pH which causes precipitation of Sr as low solubility hydroxide and carbonate phases. There was no evidence of any other phases being formed when Sr or Cs are added to metakaolin geopolymers.