Proton exchange membrane fuel cells (PEMFCs) have attracted considerable attention and applications in the field of transportation because they achieve eco-friendly electricity generation with water as the only by-product. As the preferred solid electrolyte in PEMFCs, Nafion possesses various desirable attributes and high proton conductivity, but its prohibitive cost and practical limitations in operation are problematic. Recently, several types of porous platforms, including metal–organic frameworks (MOFs), covalent organic frameworks (COFs), porous organic polymers (POPs), and hydrogen-bonded organic frameworks (HOFs) have been deployed to develop conducting systems. Post-synthetic modification for porous platforms is a flagship smart methodology in membrane electrolyte fabrication for fuel cells that concurrently combines original and other desirable features that are complementary to each other and induce enhanced conductivity. Additionally, the introduction of proton conductive mixed matrix membranes, which has recently received considerable attention as a practical method to fabricate membranes, has inspired recent research trends. This review discusses post-synthetic modification-based proton conductors and their membranes in terms of design strategies, conduction mechanisms, and diverse diagnostic modalities for future electrolyte materials in fuel cell technology.