The fast development of the bioethanol industry based on sugar cane in Colombia and Latin America has contributed to the debate on "food versus fuel" and environmental impact. In this paper, the integrated use of sugar cane bagasse was analyzed for the second generation of biofuels production, which does not affect the food supply. A case study was used to demonstrate the approach. The case study involves the conversion of 1200 tonnes/day of sugar cane bagasse to ethanol. Computer-aided process engineering tools together with exergetic and life cycle analyses using Aspen and SimaPro software were used for the screening of process configurations and the identification of opportunities for improvement. Additionally, the application of process integration principles to the selected topology identified strategies to conserve natural resources and reduce the environmental impact of the process.