Numerical investigations on the flowability of pulverized biomass are crucial for agriculture, aiding in optimizing biomass use, crop residue management, soil health improvement, and environmental impact mitigation. Rising interest in biomass and conversion processes necessitates deeper property understanding and technological process optimization. Moisture content is a key parameter influencing biomass quality. In this paper, computer simulations of shear tests depending on the moisture content using the discrete element method were carried out and compared with experimental results. An experimental study and modeling for Jenike’s direct shearing apparatus was carried out. A swelling bed model was proposed to account for the effect of moisture. The swelling bed model assumed an increase in biomass grain vorticity proportional to the moisture content. The model was solved using the discrete element method (DEM). The model considers the effect of moisture on the values of Young’s and Kirchoff’s moduli for biomass grains. The model assumed that moisture is not present in surface form, the total amount of moisture is absorbed into the interior of the material grains, and the volume of a single grain increases linearly with an increase in the volume of the absorbed moisture. The tested materials were pulverized sunflower husks, apple pomace, distiller’s dried grains with solubles (DDGS), meat and bone meal (MBM), and sawdust. Samples with moisture contents of 0%, 10%, 20%, and 30% were tested. The best agreement of the model with the experimental data was observed for the most absorbent materials in which moisture was not present in surface form, such as apple pomace, DDGS, and sawdust. Research data are important for the proper design of biomass storage, transportation equipment, and utilization as feedstock for bioenergy production or soil enrichment.