Crop-based Agri-food Supply Chains (AFSCs) are complex systems that face multiple sources of uncertainty that can cause a significant imbalance between supply and demand in terms of product varieties, quantities, qualities, customer requirements, times and prices, all of which greatly complicate their management. Poor management of these sources of uncertainty in these AFSCs can have negative impact on quality, safety, and sustainability by reducing the logistic efficiency and increasing the waste. Therefore, it becomes crucial to develop models in order to deal with the key sources of uncertainty. For this purpose, it is necessary to precisely understand and define the problem under study. Even, the characterisation process of this domains is also a difficult and time-consuming task, especially when the right directions and standards are not in place. In this chapter, a Conceptual Framework is proposed that systematically collects those aspects that are relevant for an adequate crop-based AFSC management under uncertainty.