In this study, the production of glycerol-based isobutanol is critically assessed in terms of its techno-economic performance through the estimation of economic indicators, net present value (NPV) and minimum selling price (MSP). The Monte Carlo method with Latin Hypercube Sampling (LHS) is used to propagate the market price and technical uncertainties to the economic indicator calculations and to quantify the respective economic risk. The results clearly indicated that under the given market price uncertainties, the probability of obtaining a negative NPV is 0.95. This is a very high probability of failure, which corresponds to an economic risk of 20 MM$ as a potential loss. In order to decrease the economic risk, the integrated production of isobutanol as a module added to the biodiesel plant was tested as an alternative scenario. The probability of a negative NPV is decreased from 0.95 to 0.2 and the corresponding economic risk was reduced from 20 to 0.64 MM$. Using the integrated concept of utilising the waste glycerol stream in biodiesel plants contributes to the diversification of the product portfolio for vegetable oil based biorefineries, and in turn improves cost-competitiveness and robustness against market price fluctuations.