Ocean alkalinity is critical to the uptake of atmospheric carbon in surface waters and provides buffering capacity towards the associated acidification. However, unlike dissolved inorganic carbon (DIC), alkalinity is not directly impacted by anthropogenic carbon emissions. Within the context of projections of future ocean carbon uptake and potential ecosystem impacts, especially through Coupled Model Intercomparison Projects (CMIPs), the representation of alkalinity and the main driver of its distribution in the ocean interior, the calcium carbonate cycle, have often been overlooked. Here we track the changes from CMIP5 to CMIP6 with respect to the Earth system model (ESM) representation of alkalinity and the carbonate pump which depletes the surface ocean in alkalinity through biological production of calcium carbonate and releases it at depth through export and dissolution. We report an improvement in the representation of alkalinity in CMIP6 ESMs relative to those in CMIP5, with CMIP6 ESMs simulating lower surface alkalinity concentrations, an increased meridional surface gradient and an enhanced global vertical gradient. This improvement can be explained in part by an increase in calcium carbonate (CaCO3) production for some ESMs, which redistributes alkalinity at the surface and strengthens its vertical gradient in the water column. We were able to constrain a particulate inorganic carbon (PIC) export estimate of 44–55 Tmol yr−1 at 100 m for the ESMs to match the observed vertical gradient of alkalinity. Reviewing the representation of the CaCO3 cycle across CMIP5/6, we find a substantial range of parameterizations. While all biogeochemical models currently represent pelagic calcification, they do so implicitly, and they do not represent benthic calcification. In addition, most models simulate marine calcite but not aragonite. In CMIP6, certain model groups have increased the complexity of simulated CaCO3 production, sinking, dissolution and sedimentation. However, this is insufficient to explain the overall improvement in the alkalinity representation, which is therefore likely a result of marine biogeochemistry model tuning or ad hoc parameterizations. Although modellers aim to balance the global alkalinity budget in ESMs in order to limit drift in ocean carbon uptake under pre-industrial conditions, varying assumptions related to the closure of the budget and/or the alkalinity initialization procedure have the potential to influence projections of future carbon uptake. For instance, in many models, carbonate production, dissolution and burial are independent of the seawater saturation state, and when considered, the range of sensitivities is substantial. As such, the future impact of ocean acidification on the carbonate pump, and in turn ocean carbon uptake, is potentially underestimated in current ESMs and is insufficiently constrained.