Abstract. Land and atmospheric initial conditions of the Weather Research and Forecasting (WRF) model are often interpolated from a different model output. We perform case studies during NASA's SEAC⁴RS and DISCOVER-AQ Houston airborne campaigns, demonstrating that using land initial conditions directly downscaled from a coarser resolution dataset led to significant positive biases in the coupled NASA-Unified WRF (NUWRF, version 7) surface and near-surface air temperature and planetary boundary layer height (PBLH) around the Missouri Ozarks and Houston, Texas, as well as poorly partitioned latent and sensible heat fluxes. Replacing land initial conditions with the output from a long-term offline Land Information System (LIS) simulation can effectively reduce the positive biases in NUWRF surface air temperature by ∼ 2 °C. We also show that the LIS land initialization can modify surface air temperature errors almost 10 times as effectively as applying a different atmospheric initialization method. The LIS-NUWRF-based isoprene emission calculations by the Model of Emissions of Gases and Aerosols from Nature (MEGAN, version 2.1) are at least 20 % lower than those computed using the coarser resolution data-initialized NUWRF run, and are closer to aircraft-observation-derived emissions. Higher resolution MEGAN calculations are prone to amplified discrepancies with aircraft-observation-derived emissions on small scales. This is possibly a result of some limitations of MEGAN's parameterization and uncertainty in its inputs on small scales, as well as the representation error and the neglect of horizontal transport in deriving emissions from aircraft data. This study emphasizes the importance of proper land initialization to the coupled atmospheric weather modeling and the follow-on emission modeling. We anticipate it to also be critical to accurately representing other processes included in air quality modeling and chemical data assimilation. Having more confidence in the weather inputs is also beneficial for determining and quantifying the other sources of uncertainties (e.g., parameterization, other input data) of the models that they drive.