•Engineering properties of FAGP concrete improve from 28 to 540days from casting.•Continuing gel production of FAGP concrete densify microstrucre over time.•Mechanical properties of AAS concrete decrease between 90 and 540days from casting.•Disjoining pressure & self-desiccation effect propagate cracks in AAS in long term.•FAGP concrete is behaving in a similar manor to PC concrete. This paper reports the comparison of engineering properties of alkali activated slag (AAS) and low calcium fly ash geopolymer (FAGP) concretes up to 540days. The results showed that the AAS concrete had higher compressive and tensile strength, elastic modulus and lower permeation characteristics than FAGP concrete in the initial 90days. However, a reduction in AAS concrete performance was observed between 90 and 540days, while an increase was noted in FAGP concrete over the same time period. The microscopy revealed that both reactions progressed beyond 90days with the slag–alkali producing excess C–S–H gel which was observed to increase the crack propagation and crack width at latter ages, attributed to the combined effect of disjoining pressure and self-desiccation. The fly ash geopolymerization also continued following an initial 24h heat curing resulting in a crack-free dense microstructure at 540days. Overall the discrepancy in microstructural development beyond 90days in the two concretes would explain the contradictory performance over the longer time frame.