<p>In this paper, we rectify inconsistencies that emerge in the WRF-Chem code when using the Goddard Chemistry Aerosol Radiation and Transport (GOCART) aerosol module. These inconsistencies have been reported and corrections have been implemented in WRF-Chem v4.1.3. Here, we use a WRF-Chem experimental setup configured over the Middle East (ME) to estimate the effects of these inconsistencies. Firstly, we show that the diagnostic output of PM<sub>2.5</sub> surface concentration was underestimated by 7% and PM10 was overestimated by 5 %. Secondly, we demonstrate that the contribution of sub-micron dust particles was underestimated in the calculation of optical properties and thus, Aerosol Optical Depth (AOD) was consequently underestimated by 25–30 %. Thirdly, we show that an inconsistency in the process of gravitational settling led to the overestimation of the dust column loadings by 4–6 %, PM10 surface concentrations by 2–4 %, and the rate of dust gravitational settling by 5–10 %. We present a methodology to calculate diagnostics that can be used to estimate the effects of these applied changes. Our corrections also help to explain the overestimation of PM<sub>10</sub> surface concentrations encountered in many WRF-Chem simulations. We also share the developed <i>Merra2BC</i> interpolator, which allows constructing initial and boundary conditions for chemical species and aerosols based on MERRA-2 reanalysis. The results of this work can be useful for those who simulate the dust cycle using the WRF-Chem model coupled with the GOCART aerosol module.</p>