Embedding superparamagnetic iron oxide nanoparticles (SPIONs) in functional thin films is of high interest for nanocomposites as well as for biomedical applications. However, there is still the need for high‐resolution mapping of the hidden nanoparticles. Magnetic force microscopy (MFM) has proved to be a suitable technique to image SPIONs at ambient conditions and provide information about spatial distribution, size, and magnetic behavior in a single pass. This work reports on high‐resolution mapping of magnetite nanoparticles of various sizes embedded in polymer films of various thicknesses. A quantification of the magnetic signals is used to determine the size of the magnetic core of the embedded nanoparticles.