Landslide-dams, which are often transient, can strongly affect the geomorphology, and sediment and geochemical fluxes, within subaerial fluvial systems. The potential occurrence and impact of analogous landslide-dams in submarine canyons has, however, been difficult to determine due to a scarcity of sufficiently time-resolved observations. Here we present repeat bathymetric surveys of a major submarine canyon, the Congo Canyon, offshore West Africa, from 2005 and 2019. We show how an ~0.09 km3 canyon-flank landslide dammed the canyon, causing temporary storage of a further ~0.4 km3 of sediment, containing ~5 Mt of primarily terrestrial organic carbon. The trapped sediment was up to 150 m thick and extended >26 km up-canyon of the landslide-dam. This sediment has been transported by turbidity currents whose sediment load is trapped by the landslide-dam. Our results suggest canyon-flank collapses can be important controls on canyon morphology as they can generate or contribute to the formation of meander cut-offs, knickpoints and terraces. Flank collapses have the potential to modulate sediment and geochemical fluxes to the deep sea and may impact efficiency of major submarine canyons as transport conduits and locations of organic carbon sequestration. This has potential consequences for deep-sea ecosystems that rely on organic carbon transported through submarine canyons.