The question of increasing biofuels production and the development of different biofuels production technologies has become controversial. On the one hand, production of corn-based biofuels creates a ‘food/feed vs. fuel’ tradeoff condition, along with subsequent uncertainties for both consumers and producers (farmers). On the other, advanced biofuels (from, e.g., switchgrass, miscanthus, algae), although acknowledged as environmentally friendly, are not available yet on a large commercial scale. In addition, the resource availability for the production of biofuels feedstocks and the question of a sustainable biofuels production are major issues impacting decision making. By using a multi-objective optimization model and fuzzy logic, the paper presents an approach of modeling sustainable biofuels production from conventional and advanced biofuels feedstocks, under the condition of limited resources and uncertainty resulting from incomplete information or missing knowledge about resource availability for biofuels production.