In this paper, the process of encapsulating solid particle(s) into liquid droplets in a high-throughput flow-focusing microchannel is investigated numerically. Open source software is used, which computes fluid flow in an Eulerian framework and particle dynamics with a Lagrangian approach. Previous studies have demonstrated that if no action is taken, particles suspended in a liquid passing through a flow-focusing microchannel will be encapsulated at random. This is perhaps unsurprising, but in one such study, less than 35% of droplets were found to contain exactly one particle. The two aims of this study are (i) to explore the flow patterns arising in a microfluidic channel and (ii) to elucidate the effect of salient governing parameters on encapsulation efficiency (i.e., the fraction of droplets encapsulating one particle) by focusing on ordering the particles before reaching the droplet generation section. Following validation against experimental reference data, the capillary number is varied across the three droplet generation regimes: squeezing, dripping, and jetting. We demonstrate that under certain conditions, an encapsulation frequency of 100% can be achieved with ordered particles, but in most cases, this is significantly lower. We examine the flow field to help understand how this non-uniform distribution of particles occurs. Notably, we find the dripping to be the best option for particle encapsulation and in this case extend the study to explore the effect of junction angle, finding that an angle of 60 ° is the most favorable. Improved understanding of the encapsulation process derived from this study can help to improve design of high-throughput droplet generation microfluidic systems.