We present a versatile, powerful, and user-friendly chemical data assimilation toolkit for simultaneously optimizing emissions and concentrations of chemical species based on atmospheric observations from satellites or suborbital platforms. The CHemistry and Emissions REanalysis Interface with Observations (CHEEREIO) exploits the GEOS-Chem chemical transport model and a localized ensemble transform Kalman filter algorithm (LETKF) to determine the Bayesian optimal (posterior) emissions and/or concentrations of a set of species based on observations and prior information using an easy-to-modify configuration file with minimal changes to the GEOS-Chem or LETKF code base. The LETKF algorithm readily allows for nonlinear chemistry and produces flow-dependent posterior error covariances from the ensemble simulation spread. The object-oriented Python-based design of CHEEREIO allows users to easily add new observation operators such as for satellites. CHEEREIO takes advantage of the Harmonized Emissions Component (HEMCO) modular structure of input data management in GEOS-Chem to update emissions from the assimilation process independently from the GEOS-Chem code. It can seamlessly support GEOS-Chem version updates and is adaptable to other chemical transport models with similar modular input data structure. A post-processing suite combines ensemble output into consolidated NetCDF files and supports a wide variety of diagnostic data and visualizations. We demonstrate CHEEREIO's capabilities with an out-of-the-box application, assimilating global methane emissions and concentrations at weekly temporal resolution and 2∘ × 2.5∘ spatial resolution for 2019 using TROPOspheric Monitoring Instrument (TROPOMI) satellite observations. CHEEREIO achieves a 50-fold improvement in computational performance compared to the equivalent analytical inversion of TROPOMI observations.