The separation of interesting biomolecules or compounds from high-cell-density suspensions has received intensive attention in the biotechnology industry. In recent years, monolithic cryogels have been suggested as a novel class of chromatographic adsorbents for the direct separation of biomolecules from such crude microbial feedstocks. However, the preparation of large-scale monolithic cryogels for industrial applications and the direct separation of compounds from high-cell-density broths on an industrial scale are challenging tasks. In this work, a strategy for the separation of biotransformation compounds from high-cell-density broths was developed by combination of the prefiltration of microbial cells using large-scale cryogels as the filter medium and chromatography followed using large-scale ion-exchange cryogels as the adsorbents. Composite cryogel disks (diameter of 143 mm) of poly(2-hydroxyethyl methacrylate) embedded with SiO2 nanoparticles (pHEMA-SiO2) and their anion-exchange supports grafted with 2-(dimethylamino)ethyl methacrylate (pHEMA-SiO2-DMAEMA) were prepared successfully. As an example, the separation of cytidine triphosphate (CTP) from a crude high-cell-density broth containing 233 g/L Saccharomyces cerevisiae cells was carried out by the prefiltration of cells using a cryogel bed packed with large-scale pHEMA-SiO2 disks followed by anion-exchange chromatography using a packed bed of the large-scale pHEMA-SiO2-DMAEMA cryogel disks. The results showed that about half of the yeast cells have been removed successfully from the crude broth by the prefiltration using pHEMA-SiO2 cryogel disks, and CTP with a high purity of 98.2% and recovery of 98.3% were achieved by anion-exchange chromatography using pHEMA-SiO2-DMAEMA cryogel disks from the dissolved feedstock filtrated thereafter, indicating that the present strategy is effective and these large-scale composite cryogels could be potentially applied as interesting filter media and chromatography adsorbents in industrial biotechnology and downstream processes.