Ethanol produced from renewable resources is widely regarded as an option to substitute traditional fossil fuels. By coupling the ethanol production to biogas production, an energy autarkic process with minimum ecological footprint can be created. Capable engineering tools are needed to design such processes due to their complexity and the integration necessary. Here, we present a modeling strategy that can serve this task as it allows the steady-state flowsheet simulation of biotechnological production of alternative fuels from renewable resources. The modeling concept is explained and applied to a small-scale self-sustaining ethanol production (1,000 t/a fuel-grade ethanol). An adjunct pinch-analysis for heat integration further demonstrates the potential of the tool developed for the investigation and design of future production of fuel and chemical raw materials.