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Abstract Bioelectrochemical systems (BES) have garnered significant attention for their applications in renewable energy, microbial fuel cells, biocatalysis, and bioelectronics. In BES, bioelectrodes are used to facilitate extracellular electron transfer among microbial biocatalysts. This study is focused on enhancing the efficiency of these processes through microcompartmentalization, a technique that strategically organizes and segregates microorganisms within the electrode, thereby bolstering BES output efficiency. The study introduces a deoxyribonucleic acid (DNA)‐based reduced graphene oxide (rGO) aerogel engineered as a bioanode to facilitate microorganism compartmentalization while providing an expanded biocompatible surface with continuous conductivity. The DNA‐rGO aerogel is synthesized through the self‐assembly of graphene oxide and DNA, with thermal reduction imparting lightweight structural stability and conductivity to the material. The DNA component serves as a hydrophilic framework, enabling precise regulation of compartment size and biofunctionalization of the rGO surface. To evaluate the performance of this aerogel bioanode, measurements of current generation are conducted using Shewanella oneidensis MR‐1 bacteria as a model biocatalyst. The bioanode exhibits a current density reaching up to 1.5 A·m⁻2, surpassing the capabilities of many existing bioanodes. With its abundant microcompartments, the DNA‐rGO demonstrates high current generation performance, representing a sustainable approach for energy harvesting without reliance on metals, polymers, or heterostructures.