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In this work, we report a numerical flow-focused study of bead magnetophoresis inside a continuous-flow microchannel in order to provide a detailed analysis of bead motion and its effect on fluid flow. The numerical model involves a Lagrangian approach and predicts the bead separation from blood and their collection into a flowing buffer by the application of a magnetic field generated by a permanent magnet. The following scenarios are modelled: (i) one-way coupling wherein momentum is transferred from the fluid to beads, which are treated as point particles, (ii) two-way coupling wherein the beads are treated as point particles and momentum is transferred from the bead to the fluid and vice versa, and (iii) two-way coupling taking into account the effects of bead volume in fluid displacement. The results indicate that although there is little difference in the bead trajectories for the three scenarios, there is significant variation in the flow fields, especially when high magnetic forces are applied on the beads. Therefore, an accurate full flow-focused model that takes into account the effects of the bead motion and volume on the flow field should be solved when high magnetic forces are employed. Nonetheless, when the beads are subjected to medium or low magnetic forces, computationally inexpensive models can be safely employed to model magnetophoresis.