This paper describes how the development of texts on regulatory deference by the Codex Alimentarius Commission (CAC) addresses relevant recommendations of the World Trade Organization (WTO) and supports Member countries of CAC in their negotiation and implementation of equivalence agreements. We consider the role and function of CAC within a rules-based multilateral framework, particularly in relation to the development and implementation of equivalence concepts. We then consider whether, through use of equivalence agreements, trade facilitation outcomes have been realised. Our hypothesis is that international standards on regulatory deference promote fair but aspirational standards and support fair practices in the trade of safe food – both vital outcomes for global food security and the achievement of many of the United Nations Sustainable Development Goals. We test this hypothesis against the framework provided by decisions of the WTO Sanitary and Phytosanitary Committee. We argue that the equivalence concepts and guidelines developed by CAC are appropriate but underutilised tools available for Member countries to strike a balance between their right to regulate to protect human, animal or plant life and health and to fulfil legitimate objectives whilst meeting their WTO obligations to avoid measures that constitute unnecessary barriers to trade.