The conversion of dissolved nutrients and carbon to organic matter by phytoplankton in the surface ocean, and its downward transport by sinking particles, produces a “biological pump” that reduces the concentration of atmospheric CO2. Global rates of organic matter export are a poor indicator of biological carbon storage however, because organic matter gets distributed across water masses with diverse pathways and timescales of return to the surface. Here we show that organic matter export and carbon storage can be related through a sequestration efficiency, which measures how long regenerated nutrients and carbon will be stored in the interior ocean before being returned to the surface. For the first time, we derive global maps of the sequestration efficiency of the biological pump at different residence time horizons. These maps reveal how regional patterns of organic matter export contribute to the biological pump, and how the biological pump responds to changes in biological productivity driven by climate change.