The microstructural analysis and durability study of geopolymer mortar is presented in this paper. A geopolymer mortar (GPM) was created by combining sodium hydroxide and sodium silicate as activators and curing the mixture at 80 °C in a 12 M sodium hydroxide solution. Compressive strength tests on GPM prepared with different amounts of fly ash (FA) and ground granulated blast furnace slag (GGBS) were conducted, and the optimal mixture was analysed with Energy-Dispersive X-Ray Spectroscopy and a Scanning Electron Microscope. As a means of determining the best mortar mix which can withstand the hostile conditions the durability analysis was conducted. Increased compressive strength can be attributed to the added blast furnace slag percentage. Because blast furnace slag is by-product of steel and iron, it possesses cementitious properties while finely ground. As a result, few characteristics of GGBS improve the compressive strength such as reduced heat of hydration, cementitious properties and pozzolanic activity. This specimen is more resistant to sulphate and acid attacks with the proper concentration of activators and curing conditions. Microstructural analysis was performed on mortar samples possessing highest and lowest compressive strength in order to determine the presence of geopolymer gel formation and the bonding behaviour of the mixture. This study can also help in better understanding of the optimization of the mixture for the desired properties in the future.