Magnetic nanoparticles (MNPs) are key elements in several biomedical applications, e.g., in cancer therapy. Here, the MNPs are remotely manipulated by magnetic fields from outside the body to deliver drugs or generate heat in tumor tissue. The efficiency and success of these approaches strongly depend on the spatial distribution and quantity of MNPs inside a body and interactions of the particles with the biological matrix. These include dynamic processes of the MNPs in the organism such as binding kinetics, cellular uptake, passage through cell barriers, heat induction and flow. While magnetic measurement methods have been applied so far to resolve the location and quantity of MNPs for therapy monitoring, these methods can be advanced to additionally access these particle–matrix interactions. By this, the MNPs can further be utilized as probes for the physical properties of their molecular environment. In this review, we first investigate the impact of nanoparticle–matrix interactions on magnetic measurements in selected experiments. With these results, we then advanced the imaging modalities magnetorelaxometry imaging and magnetic microsphere tracking to spatially resolve particle–matrix interactions.