The performance of radiant floors depends on the thermal properties of the heat transfer medium surrounding the heating pipes, which for wet construction is often an enveloping mortar. The incorporation of materials with latent heat storage properties such as Phase Change Materials (PCM), to act as thermal batteries in Radiant Floor Systems (RFS), can improve buildings’ energy efficiency and thermal comfort. However, despite the advantages of incorporating PCM into the RFS’s mortar such as the additional energy storage capacity, the PCM-containing mortars exhibit challenges related to specific heat and thermal conductivity. To evaluate the impact that the incorporation of microencapsulated PCM (mPCM) has on the thermal and energy performances of RFS, two specimens were built, one reference and one with PCM. An innovative mortar containing mPCM was applied in the PCM-RFS experimental specimen and then tested under different intermittent heating strategies controlled by: i) timer and, ii) floor surface temperature. The temperature profiles of the PCM-RFS and the operating time were compared with the reference RFS. Intermittent heating controlled by timer proved beneficial when the heating strategy is planned to combine renewable solar energy and off-peak electricity tariff. Conversely when the heat source is controlled by floor surface temperature setpoint, the thermophysical properties of the PCM-RFS impaired its performance, pointing to a mismatch between the operating conditions and the properties of the PCM.