Agri-food supply chains are subjected to many sources of uncertainty. If these uncertainties are not managed properly, they can have a negative impact on the agri-food supply chain (AFSC) performance, its customers, and the environment. In this sense, collaboration is proposed as a possible solution to reduce it. For that, a conceptual framework (CF) for managing uncertainty in a collaborative context is proposed. In this context, this paper seeks to answer the following research questions: What are the existing uncertainty sources in the AFSCs? Can collaboration be used to reduce the uncertainty of AFSCs? Which elements can integrate a CF for managing uncertainty in a collaborative AFSC? The CF proposal is applied to the weather source of uncertainty in order to show its applicability.