Submarine channels are the main conduits and intermediate stores for sediment transport into the deep sea, including organics, pollutants, and microplastics. Key drivers of morphological change in channels are upstream-migrating knickpoints whose initiation has typically been linked to episodic processes such as avulsion, bend cutoff, and tectonics. The initiation of knickpoints in submarine channels has never been described, and questions remain about their evolution. Sedimentary and flow processes enabling the maintenance of such features in non-lithified substrates are also poorly documented. Repeated high-resolution multibeam bathymetry between 2012 and 2018 in the Capbreton submarine canyon (southeastern Bay of Biscay, offshore France) demonstrates that knickpoints can initiate autogenically at meander bends over annual to multi-annual time scales. Partial channel clogging at tight bends is shown to predate the development of new knickpoints. We describe this initiation process and show a detailed morphological evolution of knickpoints over time. The gradients of knickpoint headwalls are sustained and can grow over time as they migrate through headward erosion. This morphology, associated plunge pools, and/or development of enhanced downstream erosion are linked herein to the formation and maintenance of hydraulic jumps. These insights of autogenically driven, temporally high-frequency knickpoints reveal that cut-and-fill cycles with depths of multiple meters can be the norm in submarine systems.