Replacement of Portland cement is a practical strategy to reduce concrete manufacturing CO2 emissions. However, this approach typically results in a diminished portlandite content in the hardened mix, elevating the risk of carbonation-induced corrosion in steel-reinforced concrete. Carbonation is frequently studied by exposing the samples to elevated CO2 levels ( 1% and 20%). However, the carbonation process and its by-products might differ markedly under natural conditions. In the context of RILEM TC 281-CCC ‘Carbonation of Concrete with SCMs’, a comprehensive three-year natural carbonation study on mortar samples was carried out across three laboratories. Samples were made with commercially available cement (CEM I, CEM II/B-V, CEM III/B). This study examined two natural carbonation scenarios: one in a regulated climate chamber and the other outdoors, protected from direct rainfall. The progression of carbonation was determined using a phenolphthalein indicator and compared to optical pH measurements. The phase composition was analysed by X-ray diffraction, attenuated total reflectance Fourier transform infrared spectroscopy, and thermogravimetric analysis. Additionally, the CO2 capture in three-year-old naturally carbonated samples was assessed and contrasted against the reactive CaO content. The thermogravimetric analysis data revealed a non-linear relationship between the portlandite content in the uncarbonated zone and the carbonation rate. A reduced clinker content leads to lower pH values in carbonated and uncarbonated zones. Notably, samples containing CEM II displayed the largest formation of CaCO3 which, divided by the theoretical maximum amount of CaCO3 from reactive CaO, signifies the highest degree of carbonation among the cement types studied.