We use the GEOS‐Chem four‐dimensional variational data assimilation system to estimate emissions of carbon monoxide (CO) and nitrogen oxides (NOx) in November 2009 and July 2010. We assimilated CO retrievals from The Measurements of Pollution In The Troposphere (MOPITT), ozone (O3) retrievals from the Tropospheric Emission Spectrometer (TES) and the Optical Spectrograph and InfraRed Imager System (OSIRIS), and NO2columns from the Ozone Monitoring Instrument (OMI). By assimilating data for multiple chemical species with the four‐dimensional variational scheme we obtain a consistent chemical state over the assimilation period. The modeled O3bias was reduced to less than 3.5 ppbv everywhere, relative to independent aircraft O3data, except in the high‐latitude upper troposphere and lower stratosphere. We found that in November, the CO and NOxemission estimates obtained with the multiple species assimilation were generally comparable to those inferred from assimilating only MOPITT or OMI data, respectively, whereas in July the differences were larger. For the main anthropogenic source regions, the inferred North American and European emissions responded most strongly to the multispecies information in the assimilation. In July, North American and European CO emission estimates differed by 31% and 65% relative to the MOPITT‐only estimates, respectively. We also found large differences for the North American and European NOxemission estimates, which differed by 27% and 16% relative to the OMI‐only estimates, respectively. Our results highlight the potential benefit of exploiting the additional constraints offered by multispecies chemical data assimilation. Multispecies data assimilation provides a means of indirectly estimating tropospheric OHMultispecies DA better fits assimilated MOPITT CO, whereas OMI‐only DA better fits OMI NO2dataEuropean emission estimates are most sensitive to the multispecies information in GEOS‐Chem