Using bioenergy systems in architecture provides energy by means of negative emissions technologies (NETs). It plays an important role in stabilizing CO2 emissions at low levels. This depends on options of low life cycle emissions (for instance, a sustainable use of biomass residues), and on outcomes that are site-specific and rely on efficient integrated systems that convert biomass into bioenergy. The objective of this study is to develop self-sufficient systems that generate bioelectricity and offer safety, electricity generation efficiency, cost-effectiveness, waste treatment, integration in domestic use, ease of use, reproducibility and availability. The study also intends to elaborate a general design method of embedding and utilizing microorganisms into architectural elements to achieve design ecology, introducing a multidisciplinary research application through a design theory aspect. The study is based on previous experimental work conducted by the authors. Microbial fuel cell technology was applied to exploit the natural potential of a fungal strain that was identified and optimized to be implemented in microbial fuel cells (MFCs) to generate electricity. The outcomes were included in the self-sufficient cluster design that meets the aforementioned conditions. The novelty of this study is the direct use of a bioreactor of MFCs in a design application for bioelectricity production. It aims to reduce the currently high global CO2 emissions that come from the energy supply sector (47%) and from the building sector (3%), as well as to eliminate the need for large-scale infrastructure intervention. This self-sufficient bio-electricity cluster therefore outweighs other abiotic renewable energy resources such as solar energy or wind power.