The goal of this work was to demonstrate real-time tracking of in vivo nanoparticle concentrations utilizing multispectral optoacoustic tomography (MSOT). Combining the high contrast of optical imaging with the high resolution of ultrasound imaging, MSOT was utilized for non-invasive, real-time tomographic imaging of particles in mice and the results calibrated against analysis of tissue samples with electron paramagnetic resonance (EPR) spectroscopy. In a longitudinal study, the pharmacokinetics (pK) and biodistribution of Cyanine-7 (Cy7) conjugated superparamagnetic iron oxide nanoparticles (Cy7-SPIONs) were monitored after intravenous administration into the tail vein of healthy B6-albino mice. Concentrations of Cy7-SPIONs determined by MSOT image analysis of the liver, spleen, and kidneys showed excellent agreement with EPR data obtained on tissue samples ‒ validating MSOT’s ability to quantify SPION concentrations with high spatial resolution. Both methods of analysis indicated highest accumulation of Cy7-SPIONs in the liver followed by the spleen, and negligible accumulation in the kidneys; SPION accumulation in organs with high concentrations of mononuclear phagocytic system macrophages is typical. Additionally, our study observed that particles modified with a 2 kDa polyethylene glycol (PEG) demonstrated significantly prolonged half-life in circulation compared to particles with 5 kDa PEG. The study demonstrates the potential of Cy7-SPIONs and MSOT for quantitative localization of magnetic nanoparticles in vivo, which can potentially be used to study their toxicity, quantify the efficacy of targeted drug delivery (e.g. within tumors), and their use as a multi-modal diagnostic agent to monitor disease progression.