Coastal upwelling rates are classically determined by the intensity of the upper-ocean offshore Ekman transport. But (sub)mesoscale turbulence modulates offshore transport, hence the net upwelling rate. Eddy effects generally oppose the Ekman circulation, resulting in so-called “eddy cancellation,” a process well studied in the Southern Ocean. Here we investigate how air–sea heat/buoyancy fluxes modulate eddy cancellation in an idealized upwelling model. We run CROCO simulations with constant winds but varying heat fluxes with and without submesoscale-rich turbulence. Eddy cancellation is consistently evaluated with three different methods that all account for the quasi-isopycnal nature of ocean circulation away from the surface. For zero heat fluxes the release of available potential energy by baroclinic instabilities is strongest and leads, near the coast, to nearly full cancellation of the Ekman cross-shore circulation by eddy effects, i.e., zero net mean upwelling flow. With increasing heat fluxes eddy cancellation is reduced and the transverse flow progressively approaches the classical Ekman circulation. Sensitivity of the eddy circulation to synoptic changes in air–sea heat fluxes is felt down to 125-m depth despite short experiments of tens of days. Mesoscale dynamics dominate the cancellation effect in our simulations which might also hold for the real ocean as the relevant processes act below the surface boundary layer. Although the idealized setting overemphasizes the role of eddies and thus studies with more realistic settings should follow, our findings have important implications for the overall understanding of upwelling system dynamics.