In this paper the evolution of the microstructure of Portland cement mortar is analyzed, by using electrical impedance measurements. Cement mortars are compared without and with two pozzolanic substitutions: spent fluid catalytic cracking catalyst (FCC) and metakaolin (MK). The measurement method is described and the model for analyzing the electrical impedance spectra is developed. Three electrical parameters are defined: electrical resistivity, capacitance exponent, and capacitive factor. The results show a significant increase in resistivity of the mortars with pozzolans after 7 days of curing, especially in mortars with MK. This increase is correlated with lime-fixing by the pozzolans. The capacitive properties evolve differently at early age, but reach the same values after 148 days. The electrical and mineralogical data show that the evolution of the microstructure in the mortar with MK starts before it does in the mortars with FCC and that the final microstructure becomes different.