Biofuel systems have been considered to yield more sustainable outcomes than their fossil counterparts. This chapter demonstrates that biofuels do not necessarily lead to a more sustainable outcome, such that each system warrants critical appraisal independently. Largely, preferability for biofuel systems rests on the impact under assessment, as bio-based systems are more taxing for impacts like acidification and eutrophication, but lower in climate change and toxicity. In this way, generalizations regarding the superiority or otherwise of biofuels may not support robust transitions towards sustainable production and consumptions systems. With reference to contrasting energy systems: biofuels and fossil fuels, it is shown with life cycle assessment that bioenergy systems are not always preferable for climate change. It is important to apply hard systems approaches to elucidate the merits or otherwise of production systems alternative to current fossil ones.