Reasons behind food loss can be very specific for each product and supply chain stage but it is also affected by factors independent of the product and stage. This work focuses on such generic factors and develops a framework to analyze food loss as a systemic outcome. The framework highlights the interconnected nature of problem across supply chain stages and therefore emphasizes the need to look at the whole system instead of specific stages, when proposing solutions. Practices and underlying causes contributing to food loss are identified for each stage of the supply chain using a literature search. Deductive logic is used to fill the gaps where literature was found to be scarce, and to derive socio-economic indicators that signal the presence of identified causes. Using this framework, we propose a non-exhaustive list of 30 socio-economic indicators, which can signal the presence of the 22 practices and 60 causes associated with food loss in supply chains. This list can serve as a starting list for practitioners and policymakers to build on when analyzing food losses in supply chains in their region. We evaluate the framework using a field-study of a tomato supply chain in Nigeria, and conclude that it can be a useful tool to identify practices, causes, and indicators of food loss.