Ammonia synthesis by the Haber–Bosch method is a typical and effective implementation of the chemical process in the large-scale fertiliser industry. Due to the growing demand for fertilisers and food, it is desirable to study this process thoroughly using modern numerical methods to improve the operation of existing devices and facilitate the design of new devices in industrial installations. This manuscript focuses on the influence of the catalyst bed parameters on the ammonia synthesis process. Variants with different sizes of catalyst particles and modifications of the geometry of catalytic beds were considered. The axial-radial Topsoe converter with magnetite as a catalyst, commonly used in modern fertiliser industry beds, was investigated using Computational Fluid Dynamics. As a result, contours of velocity, pressure, concentration, and rate of ammonia formation were obtained. The analysis of the obtained results made it possible to determine the gradient of ammonia production rate in the catalyst bed and designate zones with negligible reaction rates. The authors also proposed possible bed geometry modifications to reduce bed volumes without affecting the converter’s performance.