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The building sector represents around one-third of the energy related to the EU CO2eq emissions, which makes it a crucial sector for achieving the EU’s energy and environmental goals. Thus, the EU has established a legislative framework to foster, among others, the modernisation of the existing building stock through a better energy system integration. In this sense, bearing in mind the needs of energy system retrofit of the public buildings in Spain, this paper carried out a thorough analysis of different trade-off solutions obtained from the multiobjective optimization of a polygeneration system for the TR5 building of the Polytechnic University of Catalunya. The results highlight the selection of PV panels, cogeneration modules and 2nd life Li-Ion batteries, among others, to achieve cost-effective and sustainable energy systems. By covering the available area, 2000 m2, the PV panels attend about 23% of the electricity required for the building. On the other hand, considering the current geopolitical tensions, it presents a potential configuration that allows to cut off the natural gas consumption reducing about 6% the current cost. The study was carried out by using a Mixed Integer Linear Programming model maximizing the Net Present Value of the project considering the environmental impact. The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Edwin S. Pinto reports financial support was provided by Europe Union-NextGenerationEU and the Ministry of Universities of Spain.