AbstractAtmospheric CO₂ measurements from a dense surface network can help to evaluate terrestrial biosphere model (TBM) simulations of Net Ecosystem Exchange (NEE) with two key benefits. First, gridded CO₂ flux estimates can be evaluated over regional scales, not possible using flux tower observations at discrete locations for model evaluation. Second, TBM ability to explain atmospheric CO₂ fluctuations due to the biosphere can be directly tested, an important objective for anthropogenic emissions monitoring using atmospheric observations. Here, we customize the Vegetation Photosynthesis and Respiration Model (VPRM) for an eastern North American domain with strong biological activity upwind of urban areas. Parameters are optimized using flux tower observations from a historical database with sites in (and near) the domain. In addition, the respiration model (originally a linear function of temperature) is modified to account for impacts of changing foliage, non‐linear temperature, and water stress. Flux estimates from VPRM, the Carnegie‐Ames‐Stanford Approach (CASA) model and the Simple Biosphere Model v4 (SiB4), are convolved with footprints from atmospheric transport models for evaluation with CO₂ observations at 21 towers in the domain, with roughly half of the towers used here for the first time. Results show that the new respiration model in VPRM helps to correct a growing season sink bias in the atmosphere associated with underestimated summertime respiration using the original model with annual parameters. The new VPRM also better explains fine‐scale atmospheric CO₂ variability compared to other TBMs, due to higher resolution diagnostic phenology, the new respiration model, domain‐specific parameters, and high‐quality input data sets.