The Humboldt Current System (HCS) is characterized by high marine primary productivity, the dynamics of which are closely linked to climate variability. However, its changes beyond the last glacial cycle are virtually unknown due to a dearth of long sediment records. Here, we present a 500 ka multi-proxy marine productivity reconstruction from the southernmost part of the HCS (similar to 43 S). At these latitudes, marine productivity changes have been typically attributed to glacial-interglacial changes in the South Pacific Subtropical High (SPSH) and Southern Westerly Winds (SWWs). Surprisingly, our productivity reconstruction based on biomarkers and benthic foraminifera does not show recurrent glacial-interglacial variability. Instead, large increases in organic matter flux occurred during MIS 2-4 and MIS 10-11. Micronutrients in aeolian dust and Southern Ocean-sourced macronutrients seem to be unlikely drivers, as both would have led to recurrent glacial-interglacial variability as observed elsewhere. Another source of micronutrients is via continental runoff, the amount of which is controlled by Patagonian Ice Sheet variability and/or precipitation. We interpret our productivity records as reflecting changes in the amount of nutrients supplied by continental runoff, which are driven by precipitation variations linked to the configuration of the SPSH-SWWs in response to orbital forcing in the eccentricity band. During eccentricity minima, the position of SPSH changes minimally from precession minima to maxima. This SPSH-SWWs configuration probably results in a prolonged period of high precipitation, which in turn increases the continental runoff and the supply of micronutrients to the sea.