Here we present a facile and efficient method of controlled embedding of inorganic nanoparticles into an ultra-thin (<15 nm) and flat (~1.0 nm) polymeric coating that prevents unwanted aggregation. Hybrid polymer brushes-based films were obtained by simultaneous incorporation of superparamagnetic iron oxide nanoparticles (SPIONs) with diameters of 8–10 nm into a polycationic macromolecular matrix during the surface initiated atom transfer radical polymerization (SI-ATRP) reaction in an ultrasonic reactor. The proposed structures characterized with homogeneous distribution of separated nanoparticles that maintain nanometric thickness and strong magnetic properties are a good alternative for commonly used layers of crosslinked nanoparticles aggregates or bulk structures. Obtained coatings were characterized using atomic force microscopy (AFM) working in the magnetic mode, secondary ion mass spectrometry (SIMS), and X-ray photoelectron spectroscopy (XPS).