<p>Since their commercialization, packed bed reactors have become a key component of the modern chemical industry. Addressing their shortcomings would yield significant economic benefits and mitigate their negative environmental impact. This is particularly true for ammonia synthesis, a process that is performed globally on a massive scale. Packed bed reactors have a complex internal structure, with catalyst pellets randomly distributed within the reactor vessel with the pore space characteristics clearly impacting the reactor performance. In this work, we develop a three-dimensional model of a packed bed reactor with explicitly resolved catalyst pellets and apply it to ammonia synthesis. After confirming that the simulation results meet expectations, we apply our previously proposed framework to identify the pore-scale characteristics of the reactor that have the largest influence on the flow, described with the hydraulic permeability, and the reaction yield. Reasonably, our methodology indicates that most studied properties are impactful and that their changes have opposite effects on the hydraulic permeability and yield. To complete the analysis, we induce the suggested structural changes by manipulating the pellet size distributions and demonstrate that they lead to the predicted outcomes.</p>