Increasing upwelling intensity and shoaling of the oxygen minimum zone (OMZ) is projected for Eastern Boundary Upwelling Systems (EBUSs) under ocean warming which may have severe consequences for mesopelagic food webs, trophic transfer, and fish production also in the Humboldt Current Upwelling System (HUS). To improve our mechanistic understanding, from February 23, 2017 until April 14, 2017 we performed a 50 days mesocosm experiment in the northern HUS (off Callao Bay, Peru) and monitored the zooplankton development prior to and following a simulated upwelling event through the addition of deeper water of two different OMZ-influenced subsurface waters to four of in total eight mesocosms. To elucidate plankton dynamics and trophic relationships, we followed the temporal development of the mesozooplankton community in relation to that of phytoplankton, analyzed the fatty acid composition and gut fluorescence of dominant copepods, and determined the stable isotope (SI) and elemental composition (C:N) of dominant zooplankton taxa. Zooplankton samples were collected from the mesocosms over the entire experiment duration using an Apstein net (17 cm diameter, 100 µm mesh) to determine abundance and taxonomic composition of the zooplankton community, and to analyze fatty acid composition, gut fluorescence and elemental composition of dominant zooplankton. Furthermore, abundance and biomass of zooplankton groups was estimated from scanned ZooScan images.