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.