The assessment of the durability of civil engineering structures subjected to several chemical attacks requires the development of chemo-poromechanical models. The mechanical and chemical degradations depend on several factors such as the initial composition of the porous medium. A multi-scale model is used to incorporate the multi-level microstructural properties of the mortar material. The present paper aims to study the effect of morphological and local material properties uncertainties on the poroelastic and diffusive properties of mortar estimated with the help of analytical homogenization. At first, the proposed model is validated for different cement paste and mortar by comparison to experimental results and micromechanical models. Secondly, based on a literature study, sensitivity and uncertainty analysis have been developed to assess the stochastic predictions of the multi-scale model. The main result highlights the predominant impact of the cement matrix phases (C-S-H) and interfacial transition area at the mortar scale. Furthermore, the sensitive analysis underlines that the material properties induce more variability than the volume fraction.