Agri-food supply chains are of interest to the Colombian government due to their contribution to economic development and food security. The Cauca Valley in Colombia is one of the main agricultural areas in the country. Agri-food supply chains in this area face problems such as low incomes of small producers, affecting the quality of life in the countryside, and economic losses due to waste in transportation and storage. This paper addresses this problem by identifying the value contributed by the links of the producer, packaging, marketer, and end customers that are part of the chain, with the purpose of generating proposals or lines of action to improve their performance. More precisely, an integrated methodology to identify value related to providers’ waste production and its potential of re-manufacturing into by-products is proposed. The present document focuses on the problem instruction phase, which includes a qualitative characterization of the field, the definition of the decision context, and the instruction of the problem based on the interactive planning methodology. Results show the main processes that contribute to create value and the main waste production processes that would lead to the proposal of high-value by-products. This work is a first step in a general methodology that supports decision-making to enhance circular supply chain in the agri-food sector, contributing to the development of abductive OR methods of direct application in industrial decision making.