All aspects of fish supply chains have been severely affected by the COVID-19 pandemic, with jobs, income and food security at risk. In Peru, small scale fisheries are fundamental for food security, contributing to about 2/3 of all fish consumed nationally. One of the most important resources which is more affordable for local and regional consumption is hake (Merluccius gayi peruanus). This study is a first attempt to describe the small-scale hake fishery value chain and to quantify the impact of COVID-19 from March to August 2020 in two fishing communities in northern Peru. The levels of fishing and primary buying were the most affected, and we estimate that ~ 23,000 fishing trips were not conducted, ~ 1680 t of hake was not landed (83% decrease), and 620 jobs were negatively impacted during this period. The gross income of vessel owners and primary buyers decreased by ~ $US 913,000. Marked differences were observed in the way each community responded to the pandemic and in their resilience to cope with COVID-19, despite being located less than 10 km away. In El Ñuro, which relied more heavily on the international market for hake trade, the value chain was affected for longer, while in Los Órganos which supplied national markets, the chain was restored after an initial period of adjustment. Our study suggests that government efforts should focus on facilitating a formalisation process in all levels of the chain, develop indicators to monitor the resumption of activities and the inclusion of a value chain approach to small-scale fisheries management.