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Batteries are a cornerstone of modern technology that support a wide range of applications including portable electronics, electric vehicles and large-scale energy storage for renewable power systems. Despite the widespread use, commercial Li-ion batteries are limited by mineral resources of Li. The rapidly growing battery market demands for alternative battery systems, such as non-alkali metal-ion batteries, that are capable of delivering comparative energy densities. In the meantime, to improve the performance of the batteries via generating sustainable strategies has been broadly studied. Proteins being naturally evolved macromolecules that possess diverse structures and functional groups have been demonstrated to be able to transport various metallic ions inside the bio-organisms. Therefore, active studies have been carried out on the use of natural proteins (e.g., zein, soy, fibroin, bovine serum albumin, etc.) to enhance the electrochemical performance of non-alkali metal-ion batteries. This review provides a comprehensive summary of recent advances on studies of protein-based strategies for non-alkali metal-ion batteries and outlines perspectives for future sustainable electrochemical energy storage systems.