Biosynthesis methods are considered to be a promising technology for engineering new carbon‐based materials or redesigning the existing ones for specific purposes with the aid of synthetic biology. Lots of biosynthetic processes including metabolism, fermentation, biological mineralization, and gene editing have been adopted to prepare novel carbon‐based materials with exceptional properties that cannot be realized by traditional chemical methods, because microbes evolved to possess special abilities to modulate components/structure of materials. In this review, the recent development on carbon‐based materials prepared via different biosynthesis methods and various microbe factories (such as bacteria, yeasts, fungus, viruses, proteins) are systematically reviewed. The types of biotechniques and the corresponding mechanisms for the synthesis of carbon‐based materials are outlined. This review also focuses on the structural design and compositional engineering of carbon‐based nanostructures (e.g., metals, semiconductors, metal oxides, metal sulfides, phosphates, Mxenes) derived from biotechnology and their applications in electrochemical energy storage devices. Moreover, the relationship of the architecture–composition–electrochemical behavior and performance enhancement mechanism is also deeply discussed and analyzed. Finally, the development perspectives and challenges on the biosynthetic carbons are proposed and may pave a new avenue for rational design of advanced materials for the low‐carbon economy.