Surface waters in upwelling regions are thought to be nutrient rich and hence inhibit nitrogen fixation (diazotrophy) because diazotrophs can preferentially assimilate nitrate and ammonia instead of expending energy to fix dinitrogen. We found average nitrogen fixation rates to be two to seven times higher in the surface waters of the upwelling region of the eastern equatorial Atlantic than typically measured here during non‐upwelling periods. We posit that in this region, low nitrate‐phosphate ratio waters are upwelled, and an initial bloom of non‐diazotrophic phytoplankton removes recently upwelled nitrate. Thereby, diazotrophy is fuelled by residual phosphate and by a combination of aeolian and upwelled sources of iron. Annually, we estimate that approximately 47 Gmol of new nitrogen is introduced by diazotrophy in upwelled waters alone and 195 Gmol N is fixed in the equatorial Atlantic region. Our findings challenge the paradigm that the highest nitrogen fixation rates occur in oligotrophic gyres and instead provide evidence of its importance in upwelling regimes where phosphate‐ and iron‐rich waters rich are upwelled. Key Points Nitrogen fixation rates are higher during upwelling than non‐upwelling times Diazotrophy is fueled by low N:P, iron rich water that is upwelled Annually, 47 Gmol of new nitrogen is fixed in upwelled waters