The sugar and alcohol sector in Brazil stands out in the exploitation of sugarcane bioenergy nowadays through the delivery of bioelectricity surplus and ethanol as a fuel with low environmental impact. The sector has also been expanding the appraisal of bioenergy by developing anaerobic digestion of vinasse and filter cake on a commercial scale. In this context, this paper proposes an economic assessment when microalgae biodiesel production from the carbon dioxide from the ethanol plant is included in this technological portfolio. The coupling of microalgae cultivation and processing into biodiesel with a typical cane ethanol plant was simulated along with the appraisal of biogas derived from the aforementioned residues and the leftovers of microalgae after their oil extraction. The proposed design, which is energetically self-sufficient and produces electrical surplus through a cogeneration system with bagasse and biogas, had its economic performance assessed through the construction of an incremental cash flow. In order to accomplish a probabilistic analysis of the economic indicators (i.e. internal rate of return), variations and uncertainty were considered for the scaling economics of microalgae cultivation, CAPEX of the required expansions, selling price of biodiesel, and carbon credits. Thus, this paper points out the main conditioners so that microalgae bioenergy could be attractive to the sector’s cost of opportunity, besides suggestions that energy policies focused on decarbonization could pursue to enhance the technological development of such an underexploited pathway.