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Bacteria‐powered biobatteries using multiple microbial species under well‐mixed conditions demonstrate a temporary performance enhancement through their cooperative interaction, where one species produces a resource that another species needs but cannot synthesize. Despite excitement about the artificial microbial consortium, those mixed populations cannot be robust to environmental changes and have difficulty generating long‐lasting power because individual species compete with their neighbors for space and resources. In nature, microbial communities are organized spatially as multiple species are separated by a few hundred micrometers to balance their interaction and competition. However, it has been challenging to define a microscale spatial microbial structure in miniature biobatteries. Here, an innovative technique to design microscale spatial structures with microbial multispecies for significant improvement of the biobattery performance is demonstrated. A solid‐state layer‐by‐layer agar‐based culture platform is proposed, where individual microcolonies separately confined in microscale agar layers form a 3‐D spatial structure allowing for the exchange of metabolites without physical contact between the individual species. The optimized microbial co‐cultures are determined from selected hypothesis‐driven naturally‐occurring bacteria. Vertically and horizontally structured 3‐D microbial communities in solid‐state agar‐based microcompartments demonstrate the practicability of the biobattery, generating longer and greater power in a more self‐sustaining manner than monocultures and other mixed populations.