The building sector faces a challenge to find innovative and sustainable ways to increment the energy-efficiency of buildings and reduce their environmental impact. Recently, the incorporation of phase change material (PCM), based on a polymeric active phase (PEG-1000) in waste stone aggregates, has proven to be a promising option to be used for building restoration. Mortars that include PCM aggregates demonstrated to have favorable thermal properties, that would lead to a reduction of energy requirement for heating/cooling needs. However, the inclusion of aggregates impregnated by PEG causes a reduction in the mechanical properties of the mortars possibly due to (i) a lack of compatibility between aggregate and binder, or (ii) a problem with the confinement of the PEG, causing its dispersion in the mortar. Therefore, the aim of this study was to investigate the causes associated to the reduction of the mechanical properties and propose a method to prevent it. Preliminary results showed that, given its high water solubility, the PEG 1000 included in the stone aggregates tends to be washed away when these aggregates are incorporated in the mortar mixture. This hypothesis was confirmed by FTIR spectroscopy. Therefore, an additional confinement method using a layer to coat the stone aggregates impregnated by PEG 1000 was proposed in this study. Different materials were tested as coating layer: powder calcium hydroxide, milk of lime (suspension of Ca(OH)2 in water), pozzolana, and cocciopesto. Carbonated mortar samples using the proposed coated aggregates were, then, analyzed using FTIR to evaluate the efficiency of this encapsulation methodology. Preliminary results suggested a relevant improvement in terms of PEG confinement.