The application of mortars with latent heat storage capabilities has been extensively studied during the last decade. It is already proven the ability of these materials to store latent heat. These materials will reduce the HVAC (heating, ventilation, and air conditioning systems) operation time and contribute to save energy. However, the incorporation of microcapsules of phase change materials (PCM) into the mortar matrix change the internal structure, affecting its hardened state properties. Understanding these microstructural modifications can contribute to optimize the PCM content and the mortars performance. This work aims to study the relationship between the hardened state properties of mortars containing PCM and its internal microstructure. The mortars were prepared using different binders (lime, cement and gypsum) and different PCM contents. Their hardened state properties, microstructural modifications and heat storage capabilities were assessed. It was determined a strong relationship with the mortars microstructure. It was verified that a higher PCM content does not necessarily implies an increase in the latent heat transfer. The internal pore distribution plays an important role in the latent heat storage process. The use of PCM mortars proved to be an efficient strategy to develop both new and renovated sustainable buildings.