In spite of the growing concerns about food losses and waste (FLW), there is a lack of data and research on FLW along food supply chains (FSC). Frequently, the methodology used is unsatisfactory and, thus, fails to provide clear results. This article aims to identify the gaps and proposes a methodological framework for the assessment and report of FLW. A case study is used to illustrate how this methodological framework can be applied. The levels of FLW along the “traditional” tomato supply chain of Cali in Colombia are presented. Results show that unsold tomatoes are frequently used for different purposes. The physical quantity or rate of FLW appears in itself not sufficient to justify the research interest and guide policy intervention. Data may conceal more important issues as questions of safety and health risks or economic losses.