The objective of this work was to examine the changes in the microstructure and macro physical properties caused by the carbonation of normalised CEM II mortar. Samples were prepared and subjected to accelerated carbonation at 20°C, 65% relative humidity and 20% CO₂ concentration. On the microstructure scale, the evolutions of the cumulative pore volume, pore size distribution, and specific surface area during carbonation were calculated from the adsorption desorption isotherms of nitrogen. We also examined the evolution of macro physical properties such as the solid phase volume using helium pycnometry, porosity accessible to water, gas permeability, and thermal conductivity. The conflict between nitrogen porosity and water porosity results indicated that the porous domains explored using these two techniques are different and help to complementarily evaluate the effects of carbonation. This is a multi-scale study where results on microstructural changes can help to explain the evolution of macro physical properties.