Despite being the most employed polymer electrolyte for proton exchange membrane fuel cells (PEMFCs), Nafion® has several limitations: expensiveness, poor performance when exposed to temperatures higher than 80 °C, and its potential as a source of environmentally persistent and toxic compounds (i.e., per- and polyfluoroalkyl substances, known as PFASs) when disposed of. This work explores the functional and environmental performances of three potential PFAS-free alternatives to Nafion® as electrolytic membranes in PEMFCs: sulfonated graphene oxide (SGO), graphene oxide-naphthalene sulfonate (GONS), and borate-reinforced sulfonated graphene oxide (BSGO). Investigated via ATR-FTIR spectroscopy, TGA, and cross-sectional SEM, the membranes show an effective functionalization of GO and good thermal stability. Functional properties are determined via Ion Exchange Capacity (IEC) evaluation, Electrochemical Impedance Spectroscopy, and tensile tests. In terms of IEC, the innovative materials outperform Nafion® 212. Proton conductivities at 80 °C of SGO (1.15 S cm−1) and GONS (1.71 S cm−1) are higher than that of the commercial electrolyte (0.56 S cm−1). At the same time, the membranes are investigated via Life Cycle Assessment (LCA) to uncover potential environmental hotspots. Results show that energy consumption during manufacture is the main environmental concern for the three membranes. A sensitivity analysis demonstrates that the impact could be significantly reduced if the production procedures were scaled up. Among the three alternatives, SGO shows the best trade-off between proton conductivity and environmental impact, even though performance results from real-life applications are needed to determine the actual environmental consequences of replacing Nafion® in PEMFCs.