The development of genetically engineered (GE) crops has focused predominantly on enhancing conventional pest control approaches. Scientific assessments show that these GE crops generally deliver significant economic and some environmental benefits over their conventional crop alternatives. However, emerging evidence indicates that current GE crops will not foster sustainable cropping systems unless the negative environmental and social feedback effects are properly addressed. Moreover, GE crop innovations that promote more sustainable agricultural systems will receive underinvestment by seed and chemical companies that must understandably focus on private returns for major crops. Opportunities to promote crops that convey multi-faceted benefits for the environment and the poor are foundational to a sustainable food system and should not be neglected because they also represent global public goods. In this paper, we develop a set of criteria that can guide the development of GE crops consistent with contemporary sustainable agriculture theory and practice. Based on those principles, we offer policy options and recommendations for reforming public and private R&D and commercialization processes to further the potential contributions of GE crops to sustainable agriculture. Two strategies that would help achieve this goal would be to restore the centrality of the public sector in agricultural R&D and to open the technology development process to more democratic participation by farmers and other stakeholders.