The quantification of food losses and waste (FLW) has become a research hotspot in the last decade, but little work has been done to have food waste data in Latin American countries. This paper contributes to addressing this knowledge gap by examining the magnitude of FLW along the whole food supply chain (FSC) in Peru. The methodological approach was based on the top-down mass flow analysis at all steps of the FSC for the 2007–2017 period (most recently available data), including different food commodity groups (CGs), such as cereals, roots and tubers, oil seeds and pulses, fruits, vegetables, meat, fish and seafood, and milk. Results show an annual average of FLW of 12.8 million tonnes, which represents 47.76% of the national food supply. Regarding per capita quantities, the average amount of FLW was 426.56 kg per year when considering the entire FSC, and 67.34 kg per year when considering only the consumption step. This study suggests which steps of the FSC and CGs are the most promising targets for FLW reduction strategies in Peru.