Significance Virus lytic infection disrupts host cell homeostasis and takes over the cell space for virus multiplication. Viral-induced reorganization of prokaryotic cells must meet the challenge to restructure the cytoplasm open space of a small-sized cell. We discovered that the bacterial siphovirus SPP1 builds two types of independent compartments in the host cytoplasm to confine viral DNA enzymatic reactions and to store viral particles. This spatial partition responds to the requirements for exponential replication of SPP1 genomes and for the assembly of hundreds of viral particles. Its similarities to remodeling of the cell nucleus by herpesviruses led to the hypothesis that ancestral strategies used by viruses to invade the cell space were conserved to infect hosts of different domains of life.