This study aimed to analyse the effects of silica modulus (Ms modulus), Na concentration and fly ash (FA) content on the mechanical and microstructural properties of vapour-cured (at 75 °C for 8 h) ground granulated blast furnace slag (GGBFS)-based geopolymer mortars (GPMs). For this purpose, 27 different GPM mixtures with 0, 25 and 50 % percentages of FA were produced. In the mixtures, the sodium silicate and NaOH were used for the mortar production at three different Ms of 0.25, 0.5 and 1.0, and the amount of activators was determined to provide 3, 6 and 9 % Na concentration as a percentage of total precursor (GGBFS or GGBFS + FA). Experimental results showed that the optimum Ms modulus was 0.5 for the vapour-cured mortars made with 0 % FA and was 1.0 for the vapour-cured mortars produced with 25 and 50 % FA. The highest flexural strength (Fs) and compressive strength (Cs) values were achieved on the vapour-cured mortars made with 6 % Na, and 50 % FA. Besides, the Fs/Cs ratio of vapour-cured mortars were improved with increasing FA content. Scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDS) and polarized light microscopy (PLM) analyses showed that there were alterations and deteriorations in the microstructure of vapour-cured GPM matrixes exposed to high temperatures.