Viral infections continue to pose a significant challenge to global health, and the growing emergence of new pathogens underscores the need for innovative tools to study and combat viral threats. Many viruses reorganise the host cytoplasm into specialised membraneless compartments, known as viral factories, that serve as sites for genome replication and assembly. A growing body of evidence indicates that numerous RNA and DNA viruses form liquid–liquid phase separation (LLPS)– driven viral replication factories. These transient yet highly organised biomolecular condensate structures represent a central node in the virus–host interface, and their regulation could be used as a novel antiviral paradigm. Here, we introduce a novel conceptual and experimental framework based on the selective degradation of viral factories. By inducing the controlled disassembly of these replication hubs, we will reveal their contribution to viral replication and demonstrate the feasibility of targeting them as a universal antiviral strategy. This approach provides both a powerful tool to study virus–cell interactions in real time and a foundation for developing next-generation antivirals that function through precise spatial control of degradation within infected cells. Our findings highlight viral factories as an emerging paradigm for understanding and therapeutically exploiting the intracellular organisation of viral replication.