<p>Thin-film self-assembly of three-dimensional (3D) microsystems presents a compelling route to integrate complex functionalities into ultra-compact volumes; yet, strategies for incorporating tunable ion-conducting elements remain limited. Here, we introduce a strain-induced self-assembly platform that transforms lithographically patterned multilayer thin films into functional 3D coaxial Swiss-roll microtubes with total active volumes below 1 µL. A key innovation is the monolithic integration of a chemically tunable polyimide proton exchange membrane, enabling post-fabrication optimization of ionic transport that balances proton transport with mediator blocking. We further implement a dual-mode operational scheme that decouples microbial metabolism from electrochemical power generation, revealing biofouling, not chemical fouling or membrane degradation, as the dominant failure mechanism in conventional architectures. Critically, optimally treated polyimide membranes exhibit excellent recoverability after fouling, while cell-free mode operation maintains stable performance by physically excluding microorganisms from the microelectronic environment. This integrated bio-electronic microsystem achieves a volumetric power density of ~ 3.1 mW cm⁻³ within an ultra-compact footprint of 4.16 mm². Our work establishes a scalable thin-film engineering approach to create tunable, 3D bioelectronic power sources for autonomous microsystems.</p> Graphical Abstract <p></p>