Proton exchange membrane fuel cells (PEMFCs) are among the most promising clean energy conversion technologies, offering high efficiency and zero emissions. However, their large-scale commercialisation is limited by the high cost and environmental impact of conventional perfluorosulfonic acid membranes such as Nafion. In recent years, increasing attention has been directed toward biopolymer-based membranes as sustainable, low-cost, and biodegradable alternatives. This review provides a comprehensive overview of recent advances in the development and modification of biopolymer membranes, including polysaccharide-based materials such as chitosan, cellulose, gellan gum, sodium alginate, and starch, as well as protein-based materials such as keratin and collagen. Various modification strategies, including sulfonation, phosphorylation, cross-linking, and incorporation of inorganic or hybrid fillers, are analysed for their impact on key parameters, including proton conductivity, methanol permeability, and power density. Comparative data indicate that several modified biopolymer membranes achieve proton conductivities of 50 mS/cm or higher. However, higher conductivity values are generally reported for membranes primarily composed of synthetic polymers, where the biopolymer is incorporated only as an additive. In addition, some biopolymer-based membranes exhibit significantly lower methanol permeability than Nafion. The lowest reported value among the membranes discussed in this article is 0.98 × 10⁻¹⁶, representing the best-performing biopolymer membrane in terms of methanol permeability alone. Although many biopolymer membranes demonstrate relatively poor performance in single PEMFC tests, several have achieved power densities comparable to Nafion, while simultaneously offering improved environmental compatibility and sustainability. Finally, current challenges and future directions are discussed, emphasising the potential of these renewable materials to advance PEMFC technology toward more sustainable and economically viable energy systems.