This study aims to understand the impact of carbonation mechanism of C-S-H and CH in photocatalytic mortars on NOx removal efficiency. Changes in surface chemistry and microstructure induced by the carbonation of portlandite and C-S-H (AFm/AFt) were correlated with the photocatalytic efficiency of the mortars doped with three types of titania-based photocatalysts. Furthermore, the influence of cementitious matrix on the photocatalytic selectivity was evaluated by studying the capacity of hydration/carbonation products to adsorb NO2. The study revealed that in terms of both photocatalytic efficiency and selectivity, mortars with microsilica addition exhibit superior properties over the pure cement-based mortars upon carbonation. Carbonation of C-S-H (AFm/AFt) gel results in the formation of capillary pores between10–50 nm, which outbalances the shielding effects of carbonates formed, leading to the enhanced photocatalytic properties. Moreover, C-S-H gel maintains its high NO2 adsorption capacity even after carbonation, resulting in the high selectivity of the photocatalysis.