Interannual variability of the ocean carbon sink is often assessed using annual air–sea carbon fluxes, but the drivers of the variability may instead arise from seasonal processes that are neglected in the annual average. The seasonal cycle largely modulates air–sea carbon exchange, hence understanding seasonal mechanisms and their link to interannual variability is necessary to determine long-term changes in the ocean carbon sink. We contrast carbon fluxes from an Earth System Model large ensemble and an observation-based ensemble to assess the representation of annual and seasonal carbon fluxes in two distinct ocean regions—the North Atlantic basin and the Southern Ocean and investigate if seasonal variability can help diagnose interannual variability. Both ensembles show strong agreement in their annual mean fluxes. However, discrepancies between the two ensembles are one to two times greater for the seasonal fluxes than the annual fluxes in the North Atlantic basin and three to four times greater in the Southern Ocean. These seasonal discrepancies compensate in the annual mean, obscuring significant seasonal mismatches between the ensembles, particularly in the Southern Ocean. A solid understanding of seasonal variability can be leveraged to diagnose interannual variability of carbon fluxes where necessary observational constraints have been built, for example, in the North Atlantic basin, where boreal winter and spring drive the interannual variability. However, in a data-sparse region like the Southern Ocean, both ensembles disagree substantially in their representations of seasonal carbon fluxes and variability, and currently, seasonal variability is of limited use in diagnosing the interannual variability of carbon fluxes in the Southern Ocean.