We present new nitrogen isotope data from the water column and surface sediments for paleo–proxy validation collected along the Peruvian and Ecuadorian margins between 1°N and 18°S. Productivity proxies in the bulk sediment (organic carbon, total nitrogen, biogenic opal, C37 alkenone concentrations) and 15N/14N ratios were measured at more than 80 locations within and outside the present-day Peruvian oxygen minimum zone (OMZ). Microbial N-loss to N2 in subsurface waters under O2 deficient conditions leaves a characteristic 15N-enriched signal in underlying sediments. We find that phytoplankton nutrient uptake in surface waters within the high nutrient, low chlorophyll (HNLC) regions of the Peruvian upwelling system influences the sedimentary signal as well. How the δ15Nsed signal is linked to these processes is studied by comparing core-top values to the 15N/14N of nitrate and nitrite (δ15NNOx) in the upper 200 m of the water column. Between 1°N and 10°S, subsurface O2 is still high enough to suppress N-loss keeping δ15NNOx values relatively low in the subsurface waters. However δ15NNOx values increase toward the surface due to partial nitrate utilization in the photic zone in this HNLC portion of the system. δ15Nsed is consistently lower than the isotopic signature of upwelled NO3−, likely due to the corresponding production of 15N depleted organic matter. Between 10°S and 15°S, the current position of perennial upwelling cells, HNLC conditions are relaxed and biological production and near-surface phytoplankton uptake of upwelled NO3− are most intense. In addition, subsurface O2 concentration decreases to levels sufficient for N-loss by denitrification and/or anammox, resulting in elevated subsurface δ15NNOx values in the source waters for coastal upwelling. Increasingly higher production southward is reflected by various productivity proxies in the sediments, while the north–south gradient towards stronger surface NO3− utilization and subsurface N-loss is reflected in the surface sediment 15N/14N ratios. South of 10°S, δ15Nsed is lower than maximum water column δ15NNOx values most likely because only a portion of the upwelled water originates from the depths where highest δ15NNOx values prevail. Though the enrichment of δ15NNOx in the subsurface waters is unambiguously reflected in δ15Nsed values, the magnitude of δ15Nsed enrichment depends on both the depth of upwelled waters and high subsurface δ15NNOx values produce by N-loss. Overall, the degree of N-loss influencing subsurface δ15NNOx values, the depth origin of upwelled waters, and the degree of near-surface nitrate utilization under HNLC conditions should be considered for the interpretation of paleo δ15Nsed records from the Peruvian oxygen minimum zone.