Fly-ash based geopolymers have been considered as a low-cost yet effective adsorbent for the removal of heavy metal cations, including Cu2+, from the aqueous environment. In the synthesis of geopolymers, the fly-ash needs to be alkali activated using several systems rich in either Na+ or K. Herein, we investigate the effect of alkali activation on the structural alteration and its consequence on the adsorption capacity. Based on the series of detailed characterizations, the geopolymers formed in Na+-based alkali system is found to have more organized structure compared to that formed in K+-based alkali system. Moreover, the incorporation of additional silicate creates ancillary structure which positively contributes to the organization of the overall structure. All the samples, fly-ash and geopolymers, exhibits Cu2+ adsorption based on Langmuir isotherm and pseudo-second order kinetic. The geopolymers with more organized structure display higher Cu2+ adsorption capacity, which reaches 40 mg g(-1) higher in comparison to 7 mg g(-1) for fly ash sample. The structural alteration induces the formation of open-framework structure with more accessible sites which can accommodate more Cu2+. Our study provides a fundamental understanding for the design and fabrication of geopolymers as an effective adsorbent for the removal of heavy metal cations.