The present study investigates the use and implementation of energy efficient measures and strategies for building applications, toward the Nearly Zero Energy Buildings target. Specifically, objective of the study is to implement building integrated photovoltaic thermal devices coupled with a phase change materials heat exchanger acting as an active thermal storage building component, with the aim to add flexibility to the building while still maintaining indoor comfort conditions. To show the potentials of the novel configuration proposed in this paper, a multi-zone grey-box model is developed and validated to capture the thermal dynamics of a building, and a control strategy applied to the whole system is developed for energy management purpose. The whole simulation model, including thermophysical properties of the building-system and the control features, is implemented in a MATLAB environment. To assess the model and application potentials toward the optimal design and operation of the proposed system for energy efficiency and flexibility goals, a suitable case study analysis is conducted. Thus, a sensitivity analysis, using an evolutionary algorithm, is performed by considering economic and energy objective functions which focuses on the reduction of the building energy demand, load variability and economic aspects. In this regard, the optimal design configuration is underlined in a way that the operation of the components can be maximized to provide flexibility to the building: in average working conditions one single layer of PCM can provide around 186.3 Wh/K per unit of temperature and width. A rule-based management strategy is proposed to prove the possibility to shift and shave the energy peaks during high energy request periods, demand response events. Finally, by considering an approximate economic calculation, the simple payback, taking into account only the positive effects on the winter management, is around 13.5 years.