We investigate the impact of biogenic emissions on carbon monoxide (CO) and formaldehyde (HCHO) in the Southern Hemisphere (SH), with simulations using two different biogenic emission inventories for isoprene and monoterpenes. Results from four atmospheric chemistry models are compared to continuous long-term ground-based CO and HCHO column measurements at the SH Network for the Detection of Atmospheric Composition Change (NDACC) sites, the satellite measurement of tropospheric CO columns from the Measurement of Pollution in the Troposphere (MOPITT), and in situ surface CO measurements from across the SH, representing a subset of the National Oceanic and Atmospheric Administration's Global Monitoring Division (NOAA GMD) network. Simulated mean model CO using the Model of Emissions of Gases and Aerosols from Nature (v2.1) computed in the frame work of the Land Community Model (CLM-MEGANv2.1) inventory is in better agreement with both column and surface observations than simulations adopting the emission inventory generated from the LPJ-GUESS dynamical vegetation model framework, which markedly underestimate measured column and surface CO at most sites. Differences in biogenic emissions cause large differences in CO in the source regions which propagate to the remote SH. Significant inter-model differences exist in modelled column and surface CO, and secondary production of CO dominates these inter-model differences, due mainly to differences in the models' oxidation schemes for volatile organic compounds, predominantly isoprene oxidation. While biogenic emissions are a significant factor in modelling SH CO, inter-model differences pose an additional challenge to constrain these emissions. Corresponding comparisons of HCHO columns at two SH mid-latitude sites reveal that all models significantly underestimate the observed values by approximately a factor of 2. There is a much smaller impact on HCHO of the significantly different biogenic emissions in remote regions, compared to the source regions. Decreased biogenic emissions cause decreased CO export to remote regions, which leads to increased OH; this in turn results in increased HCHO production through methane oxidation. In agreement with earlier studies, we corroborate that significant HCHO sources are likely missing in the models in the remote SH.