Nowadays, the use of phase change materials (PCMs) represents a novel technique employed for retrofitting facades in existing buildings, mainly to fulfil temperature comfort and building energy efficiency requirements. The present study summarizes the results of a wide series of permeability tests carried out for understanding the moisture transport phenomena by capillary action in microencapsulated-PCM (MPCM) porous cementitious composites. Particularly, twelve MPCM cement-lime mortars are analyzed, which were cast with white cement, air lime, siliceous and lightweight aggregates (LWAs), short cellulose fibers and microencapsulated paraffin waxes. A total amount of 10% and 20% of MPCM by volume was added to the plain mixtures, and physical, mechanical and thermal properties of the composites were characterized. The experimental results are employed in an inverse identification procedure aimed at unveiling the key features of the capillary action in these partly saturated MPCM porous systems. A nonlinear FEM-based model for moisture transport phenomena is used with this purpose by adopting an extended Darcy’s law. The capillary pressure is considered to control the overall diffusion-driven mechanism. The outcome of the inverse calibration allows to better understand the influence of each material component (and specially focusing on the MPCM volume fraction) on the resulting diffusion parameters, capillary pressure and the Raleigh-Ritz pore size distribution of the analyzed porous cementitious composites. The inverse calibration procedure showed that MPCM mortars with high values of the Raleigh-Ritz (B) parameter exhibit a low capillary permeability performance. Particularly, it was observed that when MPCMs are added into the analyzed mortars, an increment of the B value is numerically obtained and a subsequent reduction of the permeability performance of the composites is obtained.