The JUNGFRAU 4-megapixel (4M) charge-integrating pixel-array detector, when operated at a full 2 kHz frame rate, streams data at a rate of 17 GB s⁻¹. To operate this detector for macromolecular crystallography beamlines, a data-acquisition system called Jungfraujoch was developed. The system, running on a single server with field-programmable gate arrays and general-purpose graphics processing units, is capable of handling data produced by the JUNGFRAU 4M detector, including conversion of raw pixel readout to photon counts, compression and on-the-fly spot finding. It was also demonstrated that 30 GB s⁻¹ can be handled in performance tests, indicating that the operation of even larger and faster detectors will be achievable in the future. The source code is available from a public repository.