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<p>In this paper, we rectify inconsistencies that emerge in the Weather Research and Forecasting model with chemistry (WRF-Chem) v3.2 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 old version underestimates the PM<span class="inline-formula">_2.5</span> diagnostic output by 7 % and overestimates PM<span class="inline-formula">₁₀</span> by 5 % in comparison with the corrected one. Secondly, we demonstrate that submicron dust particles' contribution was incorrectly accounted for in the calculation of optical properties. Therefore, aerosol optical depth (AOD) in the old version was 25 %–30 % less than in the corrected one. Thirdly, we show that the gravitational settling procedure, in comparison with the corrected version, caused higher dust column loadings by 4 %–6 %, PM<span class="inline-formula">₁₀</span> surface concentrations by 2 %–4 %, and mass of the gravitationally settled dust by 5 %–10 %. The cumulative effect of the found inconsistencies led to the significantly higher dust content in the atmosphere in comparison with the corrected WRF-Chem version. Our results explain why in many WRF-Chem simulations PM<span class="inline-formula">₁₀</span> concentrations were exaggerated. We present the methodology for calculating diagnostics we used to estimate the impacts of introduced code modifications. We share the developed Merra2BC interpolator, which allows processing Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2) output for constructing initial and boundary conditions for chemical species and aerosols.</p>