Acid-based geopolymers are known for their high temperature resistance and good mechanical performances. Some compositions also exhibit water resistance, which make them suitable for outdoor applications. This work aims to understand accurately the steps occurring during the geopolymerization process, and focuses on the type of networks forming at early stages of the reaction. The sample, prepared from metakaolin and phosphoric acid, has been analyzed at different durations and temperatures during its solidification, in order to identify which compounds would crystallize. The structural characterizations have been performed using Fourier Transform InfraRed spectroscopy and X-Ray diffraction. Several Al-O-P compounds and especially AlPO4 polymorphs crystallize in these conditions. They belong to three families of aluminophosphates, and are a reliable indication of the amorphous organization of the original sample. The first one is similar to the phases that appear in the phase transition sequences of silica, the second one is composed of AlPO4-based zeolites, and the last one is characterized by the presence of aluminum in an octahedral network. The transitions between the different phases are also discussed. Finally, the water resistance of the calcined samples is improved, and the release of acidic species in the water is limited even after a calcination at low temperature.