Virus-like particles (VLPs) have become a promising platform for vaccine production. VLPs are formed by structural viral proteins that inherently self-assemble when expressed in a host cell. They represent a highly immunogenic and safe vaccine platform, due to the absence of the viral genome and its high protein density. One of the most important parameters in vaccine production is the quality of the product. A related bottleneck in VLP-based products is the presence of cellular vesicles as a major contaminant in the preparations, which will require the set up of techniques allowing for specific discrimination of VLPs from host vesicular bodies. In this work novel, to our knowledge, multifrequency (MF) atomic force microscopy (AFM) has permitted full structural nanophysical characterization by its access to the virus capsid of the HIVbased VLPs. The assessment of these particles by advanced amplitude modulation-frequency modulation (AM-FM) viscoelastic mapping mode has enhanced the imaging resolution of their nanomechanical properties, opening a new window for the study of the biophysical attributes of VLPs. Finally, the identification and differentiation of HIV-based VLPs from cellular vesicles has been performed under ambient conditions, providing, to our knowledge, novel methodology for the monitoring and quality control of VLPs.