Secular trends in coastal upwelling proxies from a sediment record at 23°S encompassing 250 years reveal two distinct stages separated by a transition period between AD 1820 and 1878. Persistent interdecadal variability that roughly follows the Pacific Decadal Oscillation is accompanied by intensification of upwelling-favourable coastal winds and decreased coastal sea surface temperature since AD 1878. We propose that an increased land-sea thermal contrast along the arid coast of northern Chile and Peru intensifies the equatorward wind stress due to reduced mean low-cloud cover, resulting in enhanced primary and export production during interdecadal El Niño-like conditions. This mechanism overcompensates for the overall effect of a regional surface warming secular trend in the Peru-Chile Current System, providing a novel insight on physical and biogeochemical feedbacks of coastal upwelling ecosystems to global warming.