Many nations obtain their energy from fossil fuels. The benefit of renewable energy is that it decreases the dependence on conventional fuel, and minimizes carbon emissions. However, the commercial feasibility of multi-biofuel production poses a major challenge. A resilient and cost-efficient biofuel supply chain network is essential for commercialization. Furthermore, disruption risks arise from operational downtime, labor strikes, natural disasters, and uncertainty embedded in the data compromise the effectiveness of tactical and strategic level supply chain planning. In line with the aforementioned requirements, a multi-biofuel supply chain network model that reduces the total system cost and accounts for both disruption and operational risks is proposed. The proposed model determines the optimal production–distribution quantities and supports facility location and capacity decisions against multiple supply and demand interruption scenarios. The lead time crashing cost is utilized here to reduce the lead time, which increases because of transportation disruptions. To decrease energy expenses and carbon emissions, a variable production rate is applied for creating an economic way to advance the manufacturing industry. The model aims to show bioenergy’s effect on making a sustainable multi-biofuel supply chain network. Two numerical examples are used to illustrate the effectiveness of the proposed model. It is seen that by utilizing the presented method, the production cost of biofuels is significantly reduced through minimized energy consumption and carbon emissions. Moreover, the impact of critical parameters on the total system cost is explained through sensitivity analysis and graphical representations. The effort provides a systematic guideline for designing various environmental, economic, and social aspects of a sustainable supply chain network for bioenergy under minimized consumption. Multi-biofuel producers, distributors, investors, and the regulators surely be benefitted from the proposed model.