We use the GEOS-Chem global 3-D model of atmospheric chemistry and transport and an ensemble Kalman filter to simultaneously infer regional fluxes of methane (CH4) and carbon dioxide (CO2) directly from GOSAT retrievals of XCH4 : XCO2, using sparse ground-based CH4 and CO2 mole fraction data to anchor the ratio. This work builds on the previously reported theory that takes into account that (1) these ratios are less prone to systematic error than either the full-physics data products or the proxy CH4 data products; and (2) the resulting CH4 and CO2 fluxes are self-consistent. We show that a posteriori fluxes inferred from the GOSAT data generally outperform the fluxes inferred only from in situ data, as expected. GOSAT CH4 and CO2 fluxes are consistent with global growth rates for CO2 and CH4 reported by NOAA and have a range of independent data including new profile measurements (0–7 km) over the Amazon Basin that were collected specifically to help validate GOSAT over this geographical region. We find that large-scale multi-year annual a posteriori CO2 fluxes inferred from GOSAT data are similar to those inferred from the in situ surface data but with smaller uncertainties, particularly over the tropics. GOSAT data are consistent with smaller peak-to-peak seasonal amplitudes of CO2 than either the a priori or in situ inversion, particularly over the tropics and the southern extratropics. Over the northern extratropics, GOSAT data show larger uptake than the a priori but less than the in situ inversion, resulting in small net emissions over the year. We also find evidence that the carbon balance of tropical South America was perturbed following the droughts of 2010 and 2012 with net annual fluxes not returning to an approximate annual balance until 2013. In contrast, GOSAT data significantly changed the a priori spatial distribution of CH4 emission with a 40 % increase over tropical South America and tropical Asia and a smaller decrease over Eurasia and temperate South America. We find no evidence from GOSAT that tropical South American CH4 fluxes were dramatically affected by the two large-scale Amazon droughts. However, we find that GOSAT data are consistent with double seasonal peaks in Amazonian fluxes that are reproduced over the 5 years we studied: a small peak from January to April and a larger peak from June to October, which are likely due to superimposed emissions from different geographical regions.