Freckle formation was directly simulated in three dimensions with a microstructure level model for unidirectional solidified Pb–Sn alloys. The microscale solidification model resolves the complex interaction of solute partition, interdendritic thermosolutal convection, dendrite formation and remelting. These simulations show that it is competition between all off these phenomena at the microstructural level that determines both the initiation and survival of solute channels and, hence, the propensity for freckle formation. The solute enriched interdendritic flow remelts both primary and secondary arms, and can deflect the primaries. This enables solutal channels to become self-sustaining, forming freckles. The microstructural model was then applied to predict the critical Rayleigh number, with excellent agreement with a large range of experimental data, demonstrating its potential for applications to new alloy systems and solidification processes.