This registration documents the protocol for the systematic review component of a design-science study developing a governance-aware reference model for deep circularity in agri-food supply chains, with an empirical focus on Nigeria. The review characterises the existing literature on circular economy in agri-food supply chains in order to establish, on quantified grounds, three research gaps: the absence of governance-aware, reference-model-based approaches to deep circularity in African agri-food chains; the absence of formal circular workflow-pattern libraries suited to fragmented and informal settings; and the disconnection of urban-organic-waste nutrient loops from supply-chain reference modelling and governance. The review follows PRISMA 2020 reporting guidelines. Its findings inform the design requirements of the reference model reported in the associated paper.