The Chicxulub impact caused a crash in export productivity in much of the world's oceans which contributed to the extinction of 75% of marine species. In the immediate aftermath of the extinction, local export productivity was highly variable, with some sites, including the Chicxulub crater, recording elevated export production. The long-term transition back to more stable export productivity regimes has been poorly documented. Here, we present elemental abundances, foraminifer and calcareous nannoplankton assemblage counts, total organic carbon, and stable carbon isotopes from the Chicxulub crater to reconstruct long-term changes of productivity over the first 3 Myr of the Paleocene. We show that export production was elevated for the first 320 kyr of the Paleocene and then declined over the next ~900 kyr, remaining low thereafter. This interval is associated with fluctuations in water column stratification and terrigenous flux, but these variables are uncorrelated to export productivity. Instead, we suggest that the turnover in the phytoplankton community from a post-extinction assemblage dominated by picoplankton (which promoted nutrient recycling in the euphotic zone) to a more normal Paleocene pelagic community dominated by calcareous nannoplankton (which more efficiently removed nutrients from surface waters and led to oligotrophy) is responsible for the decline in export production in the southern Gulf of Mexico.