In this study, different process schemes were designed and evaluated for biodiesel production from engineered cane lipids with uncertain fatty acid compositions. Four different process schemes were compared under (i) thermal glycerolysis and (ii) enzymatic glycerolysis approaches. These schemes were based on the biodiesel yield and economic indicators such as the net present value (NPV) and the minimum selling price (MSP) of biodiesel. A scheme with polar lipid separation under thermal glycerolysis resulted in the maximum NPV ($96.5 million) and minimum MSP ($1107/ton biodiesel), respectively. Through local sensitivity analysis, it was concluded that the cane lipid percentage is the most significant factor influencing process economics. A conjoint analysis of the lipid procurement price and cane lipid percent suggested that 15% cane lipids with a low lipid procurement price ($0.536/kg) results in a positive NPV. When the cane lipid price is higher (>$0.80/kg), a 20% lipid content should be considered to achieve a positive NPV. At 20% cane lipids, the worst-case and best-case scenarios were evaluated by analyzing the interplay of the three most important parameters, The best-case scenario revealed that the minimum NPV under any process scheme could yield more than $100 million (or MSP: $0.80/L), and the worst-case analysis showed that losses incurred by the plant could be as high as $80 million (MSP: $1.36/L). A Monte Carlo simulation indicated that there is a 70% chance of the plant being profitable (NPV > 0).