This study aimed to present the current state of research about the terminology, chemical reactions, mechanisms, and microstructure modelling of geopolymer binders. Modelling the structure of the geopolymerization products is essential for controlling the product properties. The currently available models have shown some limitations in determining the rate of geopolymerization and setting time of the gel. There is a need for deeper knowledge regarding the physicochemical analysis of geopolymer binders. Most of the available models have used pure material like metakaolin; however, the less pure materials are expected to have different mechanisms. The FTIR and MAS-NMR analysis are considered as effective tools in providing information on the molecular deviations during geopolymerization. However, XRD analysis is not effective because most of the changes take place in amorphous phases. Also, the role of the iron oxides and some of the other impurities still not clear where none of the previous method of investigation can be used to detect the molecular changes of the iron compounds. This issue is very relevant hence the iron oxides are existed in substantial amounts in most of the waste materials that are suitable to be used as geopolymer source materials.