Large eddy simulation is used to investigate the flashback mechanism caused by the combustion-induced vortex breakdown (CIVB) in a high-pressure lean-burn annular combustor with lean direct injection of kerosene. A single sector of the geometry, including a central pilot flame surrounded by a main flame, is simulated at takeoff conditions. A previously developed flamelet-based approach is used to model turbulence–combustion interactions due to its relatively low cost, allowing to simulate a sufficiently long time window. In stable operations, the flame stabilizes in an M-shape configuration and a periodic movement of the pilot jet, with the corresponding formation of a small recirculation bubble, is observed. Flashback is then observed, with the flame accelerating upstream toward the injector as already described in other studies. This large eddy simulation (LES), however, reveals a precursor partial blow-out of the main flame induced by a cluster of vortices appearing in the outer recirculation region. The combined effect of vortices and sudden quenching alters the mixing level close to the injector, causing first the main, then the pilot flame, to accelerate upstream, and initiate the CIVB cycle before the quenched region can re-ignite. Main and pilot flames partly extinguish as they cross their respective fuel injection point, and re-ignition follows due to the remnants of the reaction in the pilot stream. The process is investigated in detail, discussing the causes of CIVB-driven flashback in realistic lean-burn systems.