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The biogenic volatile organic compounds isoprene and α‐pinene are abundant over the Amazon and can be efficiently transported to the upper troposphere by deep convective clouds (DCC). We simulate their transport and chemistry following DCC updrafts and upper tropospheric outflow using a multi‐phase chemistry model with aerosol microphysics constrained by recent field measurements. In the lightning‐ and NO‐rich early morning outflow, organonitrates dominate the predicted ultra‐ and extremely‐low‐volatility organic compounds (ULVOCs+) derived from isoprene and α‐pinene. Nucleation of particles by α‐pinene‐derived ULVOCs+ alone, with an associated formation rate of 1.7 nm molecular clusters of 0.0006 s−1 cm−3 and resulting maximum particle number concentration of 19 cm−3, is not sufficient to explain ultrafine aerosol abundances observed in Amazonian DCC outflow. When isoprene‐derived ULVOCs+ are allowed to contribute to nucleation, the new particle formation rate increases by six orders of magnitude, and the predicted number concentrations reach 104 cm−3, consistent with observations. Plain Language Summary: Isoprene and pinene are reactive organic gases emitted by plants and are abundant over forest ecosystems such as the Amazon. Deep convective clouds can efficiently transport them higher than 10 km altitude in the atmosphere. Using a computer model, we simulate their transport, chemistry, and the subsequent formation of nanometer‐size particles in the cloud outflow. In the early morning, organic compounds containing nitrogen dominate the isoprene and pinene chemistry. We find that the reaction products develop the properties necessary to form nanoparticles, which can grow into condensation nuclei for cloud droplets. Our simulations show that the great abundance of nanoparticles observed high over the Amazon cannot be explained by pinene chemistry, as assumed previously. When isoprene‐derived species are allowed to contribute to particle formation in the model, the predicted concentrations of nanoparticles match the observations. Key Points: Isoprene nitrates dominate the ultra‐low volatility organic compounds in the day‐time tropical upper troposphereNucleation of isoprene nitrates may exceed monoterpene‐based nucleation by multiple orders of magnitude [ABSTRACT FROM AUTHOR]