The use of diesel fuel in crop and transportation operations is responsible for one third of the carbon emissions in sugarcane biorefineries. A possible solution is to replace it with biodiesel from lipids, directly produced from sugarcane by highly productive heterotrophic microalgae. In this study a heterotrophic microalgae biodiesel plant, integrated with a typical Brazilian sugarcane bio-refinery, was designed and evaluated. Molasses, steam, and electricity from sugarcane processing were used as inputs for microalgae production. For a non-integrated plant, the production cost of the microalgae biodiesel was estimated at 2.51 and 2.27 $/liter for fed-batch and continuous processes, respectively. Equipment for cultivation and carbon sources was the highest cost affecting the financial feasibility of the proposed design. For the integrated plant, at present ethanol and biodiesel selling prices, the profitability would be lower than a first-generation sugarcane bio-refinery using fossil diesel fuel for its operations. However, the CO₂ emissions would be reduced by up to 50 000 × 10³ kg per year at a cost of $83 10⁻³ kg⁻¹ CO₂-eq. If carbon credits are considered, the process becomes economically profitable even at present fuel prices.