Proton exchange membrane fuel cells (PEMFCs) are an attractive green technology for energy generation. The poor stability and performances under working conditions of the current electrolytes are their major drawbacks. Metal-Organic Frameworks (MOFs) have recently emerged as an alternative to overcome these issues. Here, we propose a robust Zr-phosphonate MOF (UPG-1) bearing labile protons able to act a priori as an efficient electrolyte in PEMFCs. Further, in an attempt to further enhance the stability and conductivity of UPG-1, a proton carrier (the amino acid Lysine, Lys) was successfully encapsulated within its porosity. The behaviors of both solids as an electrolyte were investigated by a complete experimental (impedance spectroscopy, water sorption) and computational approach (MonteCarlo, water sorption). Compared with the pristine UPG-1, the newly prepared Lys@UPG-1 composite showed similar proton conductivity but a higher stability, which allows a better cyclability. This improved cyclability is mainly related to the different hydrophobic-hydrophilic balance of the Lys@UPG-1 and UPG-1 and the steric protection of the reactive sites of the MOF by the Lys.