Upwelling of nutrient-rich waters into the sunlit surface layer of the ocean supports high primary productivity in eastern boundary upwelling systems (EBUSs). However, subsurface waters contain not only macronutrients (N, P, Si) but also micronutrients, organic matter and seed microbial communities that may modify the response to macronutrient inputs via upwelling. These additional factors are often neglected when investigating upwelling impacts on surface ocean productivity. Here, we investigated how different components of upwelled water (macronutrients, organic nutrients and seed communities) drive the response of surface plankton communities to upwelling in the Peruvian coastal zone. Results from our short-term (10 d) study show that the most influential drivers in upwelled deep water are (1) the ratio of inorganic nutrients (NOx : PO43-) and (2) the microbial community present that can seed heterogeneity in phytoplankton succession and modify the stoichiometry of residual inorganic nutrients after phytoplankton blooms. Hence, this study suggests that phytoplankton succession after upwelling is modified by factors other than the physical supply of inorganic nutrients. This would likely affect trophic transfer and overall productivity in these highly fertile marine ecosystems.