The Chicxulub bolide impact 66 million years ago drove the near-instantaneous collapse of ocean ecosystems. The devastating loss of diversity at the base of ocean food webs probably triggered cascading extinctions across all trophic levels(1-3) and caused severe disruption of the biogeochemical functions of the ocean, and especially disrupted the cycling of carbon between the surface and deep sea(4,5). The absence of sufficiently detailed biotic data that span the post-extinction interval has limited our understanding of how ecosystem resilience and biochemical function was restored; estimates(6-8) of ecosystem 'recovery' vary from less than 100 years to 10 million years. Here, using a 13-million-year-long nannoplankton time series, we show that post-extinction communities exhibited 1.8 million years of exceptional volatility before a more stable equilibrium-state community emerged that displayed hallmarks of resilience. The transition to this new equilibrium-state community with a broader spectrum of cell sizes coincides with indicators of carbon-cycle restoration and a fully functioning biological pump(9). These findings suggest a fundamental link between ecosystem recovery and biogeochemical cycling over timescales that are longer than those suggested by proxies of export production(7,8), but far shorter than the return of taxonomic richness(6). The fact that species richness remained low as both community stability and biological pump efficiency re-emerged suggests that ecological functions rather than the number of species are more important to community resilience and biochemical functions.