Atmospheric carbon monoxide (CO) and nitrogen oxides (NOx = NO + NO2) emissions estimated from inverse modeling analyses exhibit large uncertainties, due, in part, to discrepancies in the tropospheric chemistry in atmospheric models. We attempt to reduce the uncertainties in CO and NOx emission estimates by constraining the modeled abundance of CO, ozone (O3), nitrogen dioxide (NO2), nitric acid (HNO3), and formaldehyde (HCHO), which are constituents that play a key role in tropospheric chemistry. Using the GEOS-Chem four-dimensional variational (4D-Var) data assimilation system, we estimate CO emissions by assimilating observations of CO from the Measurement of Pollution In the Troposphere (MOPITT), together with observations of O3 from the Optical Spectrograph and InfraRed Imager System (OSIRIS) and IASI, NO2 and HCHO from the Ozone Monitoring Instrument (OMI), and HNO3 from the Microwave Limb Sounder (MLS). Although our focus is on quantifying CO emission estimates, we also infer surface emissions of nitrogen and isoprene. Our results reveal that this multiple species chemical data assimilation produces a chemical consistent state that effectively adjusts the CO-O3-OH coupling in the model. The O3-induced changes in OH are particularly large in the tropics. We show that the analysis results in a tropospheric chemical state that is better constrained. Our experiments also evaluate the inferred CO emission estimates from major anthropogenic, biomass burning and biogenic sources.