To establish a routine workflow for in vivo magnetic resonance imaging (MRI) of mice infected with bacterial biosafety level 2 pathogens and to generate a mouse model for systemic infection with Staphylococcus aureus suitable for monitoring by MRI. A self-contained acrylic glass animal bed complying with biosafety level 2 requirements was constructed. After intravenous infection with 105 colony-forming units (CFU) (n = 3), 106 CFU (n = 11) or 107 CFU (n = 6) of S. aureus strain Newman, female Balb/c mice were whole-body scanned by 7T MRI. Abdominal infections such as abscesses were visualized using a standard T2-weighted scan. Infection monitoring was performed for each animal by measurements at 1, 3, and 7 days after infection. Intravenous pathogen application led to a dose-dependent decrease in survival probability (p = 0.03). In the group with the highest infectious dose the 7-day survival rate was 33 %. An intermediate S. aureus dose showed a survival rate of 80 %, whereas at the lowest infection dose, none of the animals died. All animals with the highest infection dose exhibited hepatic abscesses 4 days after inoculation, 80 % developed renal abscesses on the 3rd day. Mice obtaining the intermediate S. aureus load reached a plateau at day 4 with 72 % liver and 60 % renal abscess probability. No abscesses were observed in other abdominal organs at any time point. The implemented experimental setup provides a suitable and reliable in vivo MRI method to study murine abdominal infection models using BSL-2 pathogen. Systemic Staphylococcus aureus infection leads to a dose-dependent development of hepatic and renal abscesses.