The Amazon rainforest is the largest source of isoprene emissions to the atmosphere globally. Under low nitric oxide (NO) conditions (i.e. at NO mixing ratios less than about 40 pptv){,} isoprene reacts rapidly with hydroxyl (OH) to form isoprene-derived peroxy radicals (ISOPOO){,} which subsequently react with the hydroperoxyl radical (HO2) to form isoprene epoxydiols (IEPOX). IEPOX compounds are efficient precursors to the formation of secondary organic aerosols (SOA). Natural isoprene emissions{,} therefore{,} have the potential to influence cloudiness{,} rainfall{,} radiation balance and climate. Here{,} we present the first seasonal analysis of isoprene emissions and concentrations above the Amazon based on eddy covariance flux measurements made at a remote forest location. We reveal the forest to maintain a constant emission potential of isoprene throughout the year (6.9 mg m−2 h−1). The emission potential of isoprene is calculated by normalising the measured fluxes to a set of standard conditions (303 K and 1500 μmol m−2 s−1). During the wet season a factor of two reduction in absolute emissions was observed but this is explained entirely on the basis of meteorology and leaf area index{,} not by a change in isoprene emissions potential. Using an innovative analysis of the isoprene fluxes{,} in combination with measurements of its oxidation products and detailed chemical box-modelling{,} we explore whether concentrations of IEPOX follow the same seasonal cycle as the isoprene precursor. Our analysis implies that during the dry season (Sep–Jan) air pollution from regional biomass burning provides a modest increase in NO concentrations (indirectly inferred from a combination of other anthropogenic tracer measurements and box-modelling) which creates a competing oxidation pathway for ISOPOO; rather than forming IEPOX{,} alternative products are formed with less propensity to produce aerosol. This competition decreases IEPOX formation rates by a factor of two in the dry season compared with a scenario with no anthropogenic NO pollution{,} and by 30% throughout the year. The abundance of biogenic SOA precursors in the Amazon appears not to be dictated by the seasonality of natural isoprene emissions as previously thought{,} but is instead driven by regional anthropogenic pollution which modifies the atmospheric chemistry of isoprene.