Here, high‐throughput tomography (HiTT), a fast and versatile phase‐contrast imaging platform for life‐science samples on the EMBL beamline P14 at DESY in Hamburg, Germany, is presented. A high‐photon‐flux undulator beamline is used to perform tomographic phase‐contrast acquisition in about two minutes which is linked to an automated data processing pipeline that delivers a 3D reconstructed data set less than a minute and a half after the completion of the X‐ray scan. Combining this workflow with a sophisticated robotic sample changer enables the streamlined collection and reconstruction of X‐ray imaging data from potentially hundreds of samples during a beam‐time shift. HiTT permits optimal data collection for many different samples and makes possible the imaging of large sample cohorts thus allowing population studies to be attempted. The successful application of HiTT on various soft tissue samples in both liquid (hydrated and also dehydrated) and paraffin‐embedded preparations is demonstrated. Furthermore, the feasibility of HiTT to be used as a targeting tool for volume electron microscopy, as well as using HiTT to study plant morphology, is demonstrated. It is also shown how the high‐throughput nature of the work has allowed large numbers of `identical' samples to be imaged to enable statistically relevant sample volumes to be studied. High‐throughput tomography, a propagation‐based phase‐contrast X‐ray imaging technique that can visualize 1 mm3 biological samples of various types at high resolution, is presented. 3D reconstructions of the imaged volumes are calculated automatically once data collection is complete. The entire process from pressing start on data collection to viewing the final data takes less than three minutes. This speed, in combination with the use of an automated sample changer to exchange the samples, truly enables high‐throughput X‐ray imaging for the first time.