Marine nitrogen (N2) fixation supports significant primary productivity in the global ocean. However, in one of the most productive regions of the world ocean, the northern Humboldt Upwelling System (HUS), the magnitude and spatial distribution of this process remain poorly characterized. This study presents a spatially resolved data set of N2 fixation rates across six coastal transects of the northern HUS off Peru (8°S–16°S) during austral summer. N2 fixation rates were detected throughout the waters column including within the Oxygen Minimum Zone (OMZ) between 12°S and 16°S. N2 fixation rates were highest where the subsurface OMZ (O2 < 20 μmol L−1) was most intense and estimated nitrogen (N) loss was highest. There, rates were measured throughout the water column. Hence, the vertical and spatial distribution of rates indicates a colocation of N2 fixation with N loss in the coastal productive waters of the northern HUS. Despite high phosphate and total dissolvable iron (TdFe) concentrations throughout the study area, N2 fixation was still generally low (1.19 ± 3.81 nmol L−1 d−1) and its distribution could not be directly explained by these two factors. Our results suggest that the distribution was likely influenced by a complex interplay of environmental factors including phytoplankton biomass and organic matter availability, and potentially iron, or other trace metal (co)-limitation of both N2 fixation and primary production. In general, our results support previous conclusions that N2 fixation in the northern HUS plays a minor role as a source of new N and to replenish the regional N loss.