This study is focused on understanding the role of molybdic species during polycondensation reactions. For this purpose, several geopolymers were synthesized using two metakaolins of different reactivities and various amounts of ammonium molybdate (0.40, 0.80 and 1.57% molar molybdenum). The reactions involved were investigated by FTIR, Raman, DTA and MAS-NMR. The results showed that the addition of Mo induces the modification of (i) the silica species negative charge balance and (ii) their nature and size, and favors perturbations toward the polycondensation reactions, which differ in terms of metakaolin reactivity. The addition of Mo species to the silicate solution counterbalances the metakaolin reactivity (the presence of an Al-rich or Si-rich network). This highlights the modification and formation roles played by molybdenum atoms, depending on the amount of ammonium molybdate added.