Abstract. We present a characterization of the chemical composition of the atmosphere of the Brazilian Amazon rainforest based on trace gas measurements carried out during the South AMerican Biomass Burning Analysis (SAMBBA) airborne experiment in September 2012. We analyzed the observations of primary biomass burning emission tracers, i.e., carbon monoxide (CO), nitrogen oxides (NOx), ozone (O3), isoprene, and its main oxidation products, methyl vinyl ketone (MVK), methacrolein (MACR), and isoprene hydroxy hydroperoxide (ISOPOOH). The focus of SAMBBA was primarily on biomass burning emissions, but there were also several flights in areas of the Amazon forest not directly affected by biomass burning, revealing a background with a signature of biomass burning in the chemical composition due to long-range transport of biomass burning tracers from both Africa and the eastern part of Amazonia. We used the [MVK + MACR + ISOPOOH] ∕ [isoprene] ratio and the hydroxyl radical (OH) indirect calculation to assess the oxidative capacity of the Amazon forest atmosphere. We compared the background regions (CO < 150 ppbv), fresh and aged smoke plumes classified according to their photochemical age ([O3] ∕ [CO]), to evaluate the impact of biomass burning emissions on the oxidative capacity of the Amazon forest atmosphere. We observed that biomass burning emissions disturb the isoprene oxidation reactions, especially for fresh plumes ([MVK + MACR + ISOPOOH] ∕ [isoprene] = 7) downwind. The oxidation of isoprene is higher in fresh smoke plumes at lower altitudes (∼ 500 m) than in aged smoke plumes, anticipating near the surface a complex chain of oxidation reactions which may be related to secondary organic aerosol (SOA) formation. We proposed a refinement of the OH calculation based on the sequential reaction model, which considers vertical and horizontal transport for both biomass burning regimes and background environment. Our approach for the [OH] estimation resulted in values on the same order of magnitude of a recent observation in the Amazon rainforest [OH] ≅ 106 (molecules cm−3). During the fresh plume regime, the vertical profile of [OH] and the [MVK + MACR + ISOPOOH] ∕ [isoprene] ratio showed evidence of an increase in the oxidizing power in the transition from planetary boundary layer to cloud layer (1000–1500 m). These high values of [OH] (1.5 × 106 molecules cm−3) and [MVK + MACR + ISOPOOH] ∕ [isoprene] (7.5) indicate a significant change above and inside the cloud decks due to cloud edge effects on photolysis rates, which have a major impact on OH production rates.