Population growth and industrialization have led to an increase in the energy needs of the planet, causing an alarming increase in fossil fuel consumption (coal, oil, and gas), drastically decreasing their availability and contributing to global warming through the accumulation of greenhouse gases. Given the energy and environmental concerns, biofuels have received considerable attention due to their potential to reduce the consumption of fossil fuels. Biodiesel is one of the most attractive biofuels owing to the similar properties to petroleum-derived diesel; it is obtained forward from renewable lipid feedstocks such as vegetable oils and microalgae. The latter has demonstrated to be the best alternative for biodiesel production, mainly due to their high growth rate; therefore, numerous efforts are focused on achieving advances to allow the industrial production of biodiesel. In this work, the modeling, simulation, and environmental evaluation of biodiesel production from microalgae via lipid extraction and transesterification method was carried out. The modeling of the process was performed based on literature data, Aspen Plus commercial software was used for the simulation and the environmental assessment was conducted following the waste reduction algorithm (WAR) that quantifies the output and generated potential environmental impact (PEI), besides allowing the PEI classification under eight different categories. The total PEI output rate was estimated at 1.89E+00 PEI/kg of product suggesting that the process does not emit residues with the potential to negatively impact the environment. Furthermore, the evaluated topology was found to have an environmentally friendly performance in terms of consuming environmental impacts as indicated by the negative value reached for the PEI generated (-1.69E-01 PEI/kg of product). Finally, the category of potential for human toxicity by ingestion reached the highest PEI value, suggesting that the substances involved in the process primarily affect human health.