Fuel cells are drawing the attention of the scientific community because they are considered a future source of energy for developing sustainable technology that enables efficient energy generation. They offer a clean and environmentally friendly energy source with a conversion efficiency of around 60%. They also assist in reducing greenhouse gas emissions, with water being the primary product. Although Nafion® is commonly used as a proton exchange membrane (PEM) in fuel cells, its high cost and non-eco-friendly nature limits its widespread application. In light of this, there is a need to develop cost-effective and eco-friendly PEMs from renewable sources. This chapter discusses carbohydrate polymer-based nanocomposite PEMs for fuel cell applications. Carbohydrate polymers such as chitosan, sodium alginate, pectin and cellulose are of particular interest due to their excellent film-forming capabilities and inherent physico-mechanical characteristics. Additionally, this chapter focuses on studies related to Direct methanol fuel cells and microbial fuel cells. It provides both fundamental concepts and the latest advancements in carbohydrate PEMs, contributing to the science and technology of fuel cells.