Staphylococcus aureus is an opportunistic pathogen causing a diverse range of human illnesses. It possesses a wide potential to develop resistance against antimicrobial agents. Additionally, biofilm-forming strains of S. aureus contribute to the contamination of medical equipment and the establishment of persistent infections. The lytic bacteriophage phi812, a member of the Herelleviridae family, possesses a wide host range, including antibiotics-resistant and biofilm-forming S. aureus strains, which makes it a suitable candidate for the treatment of staphylococcal infections. Nonetheless, it has not been approved for general clinical application because of the insufficient understanding of many aspects of phage biology. To understand the assembly mechanism of phage phi812, we conducted an examination of infected cells using cryo-electron microscopy. We used focused ion beam milling for the preparation of electron-transparent lamellas from infected S. aureus cells and cryo-electron tomography for three-dimensional reconstructions of the cell content, followed by sub-tomogram averaging of the phage assembly intermediates. The phage head assembly starts 15 minutes post-infection at the inner surface of the cytoplasmic membrane. In a short time (30 min) the cell is fully packed with phage assembly intermediates structures, empty, filling, and genome-containing heads and tails connected to fully packed heads. Sub-tomogram averaging of the assembly intermediates revealed distinct classes of phage heads that differ in size and surface features. Our findings offer structural insights into the assembly of the phage phi812 head in near-native conditions.