Today, the characterisation of the microstructure of cement-based materials using non-destructive techniques has become an important topic of study, and among them, the impedance spectroscopy has recently experienced great progress. In this research, mortars with two different contents of fly ash were exposed to four different constant temperature and relative humidity environments during a 180-day period. The evolution of their microstructure was studied using impedance spectroscopy, whose results were contrasted with mercury intrusion porosimetry. The hardening environment has an influence on the microstructure of fly ash cement mortars. On one hand, the impedance resistances R1 and R2 are more influenced by the drying of the materials than by microstructure development, so they are not suitable for following the evolution of the porous network under non-optimum conditions. On the other hand, the impedance spectroscopy capacitances C1 and C2 allow studying the microstructure development of fly ash cement mortars exposed to those conditions, and their results are in accordance with mercury intrusion porosimetry ones. Finally, it has been observed that the combined analysis of the abovementioned capacitances could be very useful for studying shrinkage processes in cement-based materials kept in low relative humidity environments.