The invention concerns a beverage preparation system (1) for preparing a beverage by injection of a liquid into an ingredient capsule, the beverage system comprising an ingredient capsule (54) and a beverage preparation machine (2, 200) having:—an injection unit (73; 204) with at least one inner through channel (75; 210) for injecting a liquid into the ingredient capsule;—operating means for causing the machine to prepare a beverage, characterized in that the machine further comprises a cleaning device (90; 220) for automatically cleaning said at least one inner through channel, said cleaning device being actuated by said operating means.