Phase change material (PCM) laden with nanoparticles has been testified as a notable contender to increase the effectiveness of latent heat thermal energy storage (TES) units during charging and discharging modes. In this study, a numerical model is developed and implemented based on the coupling between an advanced two-phase model for the nanoparticles-enhanced PCM (NePCM) and the enthalpy-porosity formulation for the transient behavior of the phase change. Therefore, a porosity source term is added to the nanoparticles transport equation to account for the particles' frozen state in regions occupied by solid PCM. This two-phase model includes three main nanoparticles’ slip mechanisms: Brownian diffusion, thermophoresis diffusion, and sedimentation. A two-dimensional model of a triplex tube heat exchanger is considered and different charging and discharging configurations are analyzed. Compared to pure PCM, results show a substantial heat transfer enhancement during the charging and discharging cycle in which a homogeneous distribution of nanoparticles is considered as the initial condition. For this case, the two-phase model predictions are superior to the ones obtained with the classical single-phase model. In the case of multi-cycle charging and discharging, a significant deterioration of the heat transfer rate is observed using the two-phase model while such assessment is senseless using the single-phase mixture model due to the physical assumptions upon which this model is formulated. The two-phase model results reveal that, for a NePCM with high nanoparticles concentration (> 1%), the melting performance during the second charging cycle is reduced by 50% compared to the first one. This performance degradation is attributed to a noteworthy non-homogeneous distribution of the nanoparticles at the beginning of the second charging cycle. The dominant nanoparticles migration mechanism, in this scenario, is the one resulting from sedimentation effects.