The emergence of food security as a key policy issue in developed nations has been concomitant with the need to reduce greenhouse gas emissions and the implementation of Environmental Management Systems in primary industries. Biotechnological interventions such as biorefinery platforms that produce chemicals and fuels provide opportunities to reconcile the security and environmental sustainability criteria increasingly sought after by governments. Indeed, sustainable and more carbon neutral options have been positively benchmarked against scenarios based solely on petrochemical feedstocks. Notably, biotechnology companies are beginning to use Environmental Management Systems employed by other industries to advocate the benefits of green technologies that employ GM, industrial enzymes and bio-materials. Management systems such as Life Cycle Analysis are providing a powerful means to measure benefits and augment change in the biotechnology sector. These methods are discussed here in the context of the emergent 21st Century debates on security. The evidence presented leads to a conclusion where biotechnologies are likely to offer increasingly high impact options for sustainability and security criteria required for food and fuel supply.