We propose a framework that enables intensive computation on ultra-low power devices with discontinuous energy-harvesting supplies. We devise an optimization algorithm that efficiently partitions the applications into smaller computational steps during high-level synthesis. Our system finds lowoverhead checkpoints that minimize recomputation cost due to power losses, then inserts the checkpoints at the design’s registertransfer level. The checkpointing rate is automatically adapted to the source’s realtime behavior. We evaluate our mechanisms on a battery-less RF energy-harvester platform. Extensive experiments targeting applications in medical implant devices demonstrate our approach’s ability to successfully execute complex computations for various supply patterns with low time, energy, and area overheads.