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Convective systems dominate the vertical transport of aerosols and trace gases. The most recent in situ aerosol measurements presented here show that the concentrations of primary aerosols including sea salt and black carbon drop by factors of 10 to 10,000 from the surface to the upper troposphere. In this study we show that the default convective transport scheme in the National Science Foundation/Department of Energy Community Earth System Model results in a high bias of 10–1,000 times the measured aerosol mass for black carbon and sea salt in the middle and upper troposphere. A modified transport scheme, which considers aerosol activation from entrained air above the cloud base and aerosol‐cloud interaction associated with convection, dramatically improves model agreement with in situ measurements suggesting that deep convection can efficiently remove primary aerosols. We suggest that models that fail to consider secondary activation may overestimate black carbon's radiative forcing by a factor of 2.