During the ACRIDICON-CHUVA field project (September–October 2014; based in Manaus, Brazil) aircraft-based in-situ measurements of aerosol chemical composition were conducted in the tropical troposphere over the Amazon using the High Altitude and Long Range Research Aircraft (HALO), covering altitudes from the boundary layer height up to 14.4 km. The submicron non-refractory aerosol was characterized by flash-vaporization/electron impact-ionization aerosol particle mass spectrometry. The results show that significant secondary organic aerosol (SOA) formation by isoprene oxidation products occurs in the upper troposphere, leading to increased organic aerosol mass concentrations above 10 km altitude. The median organic mass concentrations in the upper troposphere above 10 km range between 1.0 and 2.1 μg m −3 (referring to standard temperature and pressure; STP) with interquartile ranges of 0.6 to 3.0 μg m −3 (STP), representing 70 % of the total submicron non-refractory aerosol particle mass. The presence of isoprene epoxydiol-derived isoprene secondary organic aerosol (IEPOX-SOA) was confirmed by marker peaks in the mass spectra. We estimate the contribution of IEPOX-SOA to the total organic aerosol in the upper troposphere to be about 20 %. After isoprene emission from vegetation, oxidation processes occur at low altitudes and/or during transport to higher altitudes, which may lead to the formation of IEPOX (one oxidation product of isoprene). Reactive uptake or condensation of IEPOX on pre-existing particles leads to IEPOX-SOA formation and subsequently increasing organic mass in the upper troposphere. This organic mass increase was accompanied by an increase of the nitrate mass concentrations, most likely due to NO x production by lightning. We further found that the ammonium contained in the aerosol particles is not sufficient to neutralize the particulate sulfate and nitrate. Analysis of the ion ratio of NO + to NO 2 + indicated that nitrate in the upper troposphere exists mainly in the form of organic nitrate. IEPOX-SOA and organic nitrates are coincident with each other, indicating that IEPOX-SOA forms in the upper troposphere either on acidic nitrate particles forming organic nitrates derived from IEPOX or on already neutralized organic nitrate aerosol particles.