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The Earth's oceans are one of the largest sinks in the Earth system for anthropogenic CO2 emissions, acting as a negative feedback on climate change. Earth system models project that climate change will lead to a weakening ocean carbon uptake rate as warm water holds less dissolved CO2 and as biological productivity declines. However, most Earth system models do not incorporate the impact of warming on bacterial remineralisation and rely on simplified representations of plankton ecology that do not resolve the potential impact of climate change on ecosystem structure or elemental stoichiometry. Here, we use a recently developed extension of the cGEnIE (carbon-centric Grid Enabled Integrated Earth system model), ecoGEnIE, featuring a trait-based scheme for plankton ecology (ECOGEM), and also incorporate cGEnIE's temperature-dependent remineralisation (TDR) scheme. This enables evaluation of the impact of both ecological dynamics and temperature-dependent remineralisation on particulate organic carbon (POC) export in response to climate change. We find that including TDR increases cumulative POC export relative to default runs due to increased nutrient recycling (+∼1.3 %), whereas ECOGEM decreases cumulative POC export by enabling a shift to smaller plankton classes (−∼0.9 %). However, interactions with carbonate chemistry cause opposite sign responses for the carbon sink in both cases: TDR leads to a smaller sink relative to default runs (−∼1.0 %), whereas ECOGEM leads to a larger sink (+∼0.2 %). Combining TDR and ECOGEM results in a net strengthening of POC export (+∼0.1 %) and a net reduction in carbon sink (−∼0.7 %) relative to default. These results illustrate the degree to which ecological dynamics and biodiversity modulate the strength of the biological pump, and demonstrate that Earth system models need to incorporate ecological complexity in order to resolve non-linear climate–biosphere feedbacks.