In this work, we studied the impact of magnetic nanoparticles (MNPs) interactions with HeLa cells when they are exposed to high frequency alternating magnetic field (AMF). Specifically, we measured the nanobiomechanical properties of cell interfaces by using Atomic Force Microscopy (AFM). The Magnetite (Fe3O4) MNPs were synthesized by coprecipitation and encapsulated with silica (SiO2): Fe3O4@SiO2 and functionalized with amino groups (-NH2): Fe3O4@SiO2-NH2, by sonochemical processing. HeLa cells were incubated or not with MNPs, then exposed or not to AMF at 37 °C. A biomechanical analysis was then performed through AFM, providing the Young's modulus and stiffness of the cells. The statistical analysis (p < 0.001) showed that AMF application or MNPs interaction modify the biomechanical behavior of the cell interfaces. Interestingly, the most significant difference was found for HeLa cells incubated with Fe3O4@SiO2-NH2 and exposed to AMF, showing that local heat of these MNPs modify elasticity and stiffness.