We use a nested-grid version of the GEOS-Chem chemistry transport model, constrained by isoprene emissions from the Model of Emissions of Gases and Aerosols from Nature (MEGAN), and the Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) bottom-up inventories, to evaluate the impact that surface isoprene emissions have on formaldehyde (HCHO) air-mass factors (AMFs) and vertical column densities (VCDs) over tropical South America during 2006, as observed by the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) and Ozone Monitoring Instrument (OMI). Although the large-scale seasonal variability of monthly mean HCHO VCDs is typically unaffected by the choice of bottom-up inventory, large relative differences of up to ±45% in the HCHO VCD can occur for individual regions and months, but typically most VCD differences are of order ±20%. These relative changes are comparable to those produced by other sources of uncertainty in the AMF including aerosols and surface albedo, but less than those from clouds. In a sensitivity test, we find that top-down annual isoprene emissions inferred from SCIAMACHY and OMI HCHO vertical columns can vary by as much as ±30–50% for each instrument respectively, depending on the region studied and the a priori isoprene emissions used. Our analysis suggests that the influence of the a priori isoprene emissions on HCHO AMFs and VCDs is therefore non-negligible and must be carefully considered when inferring top-down isoprene emissions estimates over this, or potentially any other, region.