New techniques for modifying the genomes of agricultural organisms create difficult ethical challenges. We provide a novel framework to replace worn-out ethical lenses relying on ‘naturalness’ and ‘crossing species lines.’ Thinking of agricultural intervention as a ‘negotiation’ of ‘integrity’ and ‘agency’ provides a flexible framework for considering techniques such as genome editing with CRISPR/Cas systems. We lay out the framework by highlighting some existing uses of integrity in environmental ethics. We also provide an example of our lens at work by looking at the creation of ‘cisgenic’ (as opposed to ‘transgenic’) potatoes to resist late potato blight. We conclude by highlighting three distinct advantages offered by the integrity framework. These include a more fitting way to look at the practice of scientific researchers, a more inclusive way to consider ethics around agriculture, and a more flexible way to provide the ethical grounds for regulation in different cultural contexts.