Different types of agro-industrial wastes including lignocellulosic wastes, carbohydrate and protein-rich wastes, syrup wastes and glycerol wastes were explored as biodiesel feedstocks. This strategy not only can partially replace fossil fuel but also simultaneously decrease the environmental impact. This is the first report on the techno-economic analysis and CO2 emissions of biovalorization of these wastes for biodiesel production by potential oleaginous yeasts. These evaluations could help to identify potential bottlenecks and suggest suitable implementations. Process models include steps of waste preparation, yeast cultivation, harvesting and biodiesel production through direct transesterification. The evaluation results reveal that the energy intensive steps which also have high CO2 emissions are the heating steps during waste preparation and sterilization prior to yeast cultivation. The most practical and cost-effective scenario was the recycling of glycerol waste from biodiesel industry as renewable feedstocks. This process not only reduces the production cost of biodiesel but also leads to a zero-waste discharge process with low CO2 emissions.