Geopolymer cement is fast becoming a technologically important alternative to ceramics and traditional cement. However, the amorphous nature of the phases which participate in the molecular processes occurring during evolution of geopolymer gel has made nanoscale research challenging. Here, for the first time, the local structural correlations of metakaolin-based geopolymer gel have been elucidated using in situ neutron pair distribution function analysis, following the structural changes occurring due to dissolution and repolymerization molecular processes. Over the initial 17 h of reaction, the subtle structural changes observed predominantly relate to dissolution of the initial metakaolin precursor before formation of the gel. After 90 days the gel has formed and has transitioned from the initially formed geopolymer structure (gel 1) to a more stable and more ordered state (gel 2), via an increase in cross-linking within the geopolymer gel. Through analysis of precursor dissolution behavior in different activator solutions, the impact of morphology on the rate of dissolution has been postulated, with layered precursors (metakaolin) shown to behave differently than spherical precursors (fly ash) depending on the type of activator solution used. Hence, this investigation reveals the important structural changes occurring during synthesis of this new class of low-temperature ceramics.