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Increasing energy demand and the rising levels of greenhouse gas emissions have increased the necessity of bioenergy and sustainable energy generation. The sustainable bioenergy supply chain is the key to produce sustainable biofuel. This paper points to render an optimization model for planning a versatile and dependable biomass-to-bioenergy sustainable supply chain network in which crop residuals from several agricultural sectors, multi-transportation disruption modes, multi-biorefineries, multi-biogas plants, and multi-market centers are investigated for two bioenergy sources, namely biofuel and biogas. For this reason, supply chain cost optimization, emissions of feedstock transport, processing, and distributing end biofuel to respective markets are utilized. The multi-setup-multi-delivery (MSMD) concept is incorporated and lead time crashing cost is applied to minimize the lead time in this model. The carbon emission costs at all steps and the variable production rate for the production of bioenergy are included within the model. Finally, one small-scale data and another large-scale data of six agricultural areas, four biorefineries, four biogas plants, and six markets are considered to validate the model's usefulness. The model's goal is to show bioenergy's effect to make a sustainable supply chain of biofuel and biogas. The numerical results reveal that the cost of bioenergy production contributed 54.12%, a major extent of the whole cost in biorefinery and biogas plants. The transportation segment is the preeminent initiator of carbon emissions with 83.33% in the entire carbon emission within the whole supply chain. Although, transportation cost contributed 33.09% of the total cost, the multi setup-delivery-multi-delivery policy minimized the whole supply chain cost. The results provide a systematic guideline for developing a sustainable biofuel supply-chain by minimizing cost, various aspects of transportation logistics, and multi-model alternatives under reduced energy effects. • Energy demand and two approaches of biofuel and biogas production are evaluated. • Reduction of the supply chain network's total cost. • Optimizing allocation of the appropriate quantity of residual biomass and biofuel. • Reducing energy consumption by using variable production rate. • An intelligent logistics system with multi-disruption is addressed. [ABSTRACT FROM AUTHOR]