Despite growing concerns about food losses and waste (FLW), research that focuses on FLW, especially along food supply chains (FSC), frequently uses unsatisfactory methodology and fails to provide clear results. The article reviews the existing methodological gaps with the aim of proposing a methodological framework for assessing and reporting FLW. The methodological framework was applied to a case study conducted on the “traditional” tomato supply chain in Cali (Colombia) from a waste management perspective. Interviews and surveys were carried out with farmers, traders (wholesalers, middlemen) and corner stores. The quantitative levels of FLW are presented. Empirical results show that unsold tomatoes are frequently used for different purposes. The quantity or rate of FLW alone may not be sufficient to justify the research interest and guide policy intervention: data may conceal more important issues, such as questions of food safety and health risks or economic losses. From a methodological perspective, it would be interesting to test the applicability of the framework to other aspects of FLW (e.g. qualitative FLW) and to wider case studies (e.g. households).