Projections of climate change indicate an increase in the frequency and intensity of climatic hazards such as flooding and droughts, increasing the importance of understanding community vulnerability to extreme hydrological events. This research was conducted in the flood-prone indigenous community of Panaillo, located in the Ucayali region of the Peruvian Amazon, examining how the 2010–2011 flooding affected the food system at community and institutional levels. Drawing upon in-depth fieldwork using participatory research methods over multiple seasons—including semi-structured interviews (n = 74), focus groups, and seasonal food security calendar and historical timeline exercises—the flooding was documented to have created several opportunities for increased fishing and agricultural production in Panaillo. However, households lacked the resources to fully exploit the opportunities presented by the extreme conditions and increasingly turned to migration as a coping mechanism. International aid organizations were drawn to Ucayali in response to the flooding, and introduced additional programming and provided capacity-building sessions for local institutions. However, local institutions remain weak and continue to generally disregard the increasing magnitude and frequency of extremes, documented in the region over the last decade. Moreover, the long-term implications of community-level and institutional responses to the extreme flooding could increase food system vulnerability in the future. This case study highlights the importance of considering both slow and fast drivers of food system vulnerability in the aftermath of an extreme hydrological event.