Abstract. Nucleation and condensation associated with biogenic volatile organic compounds (BVOCs) are important aerosol formation pathways, yet their contribution to the upper-tropospheric aerosols remains inconclusive, hindering the understanding of aerosol climate effects. Here, we develop new schemes describing these organic aerosol formation processes in the WRF-Chem model and investigate their impact on the abundance of cloud condensation nuclei (CCN) in the upper troposphere (UT) over the Amazon Basin. We find that the new schemes significantly increase the simulated CCN number concentrations in the UT (e.g., up to ∼ 400 cm−3 at 0.52 % supersaturation) and greatly improve the agreement with the aircraft observations. Organic condensation enhances the simulated CCN concentration by 90 % through promoting particle growth, while organic nucleation, by replenishing new particles, contributes an additional 14 %. Deep convection determines the rate of these organic aerosol formation processes in the UT through controlling the upward transport of biogenic precursors (i.e., BVOCs). This finding emphasizes the importance of the biosphere–atmosphere coupling in regulating upper-tropospheric aerosol concentrations over the tropical forest and calls for attention to its potential role in anthropogenic climate change.