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Our world is facing unprecedented energy, climate, biodiversity, and food crises. Food production (agriculture) is a main driver of these crises. Many national and international policies, such as the United Nations sustainable development goals, have acknowledged the need for our food systems to be more sustainable and resilient, while operating within planetary boundaries. Research and innovation can contribute to meeting sustainability goals. Here, we focus on biotechnological advances, such as genome editing techniques, as they provide new tools that complement the farmers’ toolbox to improve the sustainability of agricultural systems. However, regulatory requirements to ensure the safety of emerging technologies can hamper innovation, so there is a need to reconcile innovation and precaution. While safety is a prerequisite for sustainability, regulatory requirements (and thus risk assessments) should remain proportionate to risk. There is an ongoing debate on whether sustainability requirements should be considered in the pre-market authorisation process of emerging technologies. Since sustainability is a highly complex systems approach, it is most challenging to assess the potential contribution of individual products or even potential future products to sustainability. Therefore, the way forward is to define a set of incentives for a more sustainable use of existing and new products, together with a transparent and inclusive process to improve public acceptance for innovative technologies. This will ensure that opportunities are not missed out and policy goals, such as food security and the safety for human, animal, plant and environmental health can be achieved.