Climate change has led to intensification and poleward migration of the Southeastern Pacific Anticyclone, forcing diverging regions of increasing, equatorward and decreasing, poleward coastal phytoplankton productivity along the Humboldt Upwelling Ecosystem, and a transition zone around 31° S. Using a 20-year dataset of barnacle larval recruitment and adult abundances, we show that striking increases in larval arrival have occurred since 1999 in the region of higher productivity, while slower but significantly negative trends dominate poleward of 30° S, where years of recruitment failure are now common. Rapid increases in benthic adults result from fast recruitment–stock feedbacks following increased recruitment. Slower population declines in the decreased productivity region may result from aging but still reproducing adults that provide temporary insurance against population collapses. Thus, in this region of the ocean where surface waters have been cooling down, climate change is transforming coastal pelagic and benthic ecosystems through altering primary productivity, which seems to propagate up the food web at rates modulated by stock–recruitment feedbacks and storage effects. Slower effects of downward productivity warn us that poleward stocks may be closer to collapse than current abundances may suggest.