A safe and effective use of nanoparticles in biology and medicine requires a thorough understanding, down to the molecular level, of how nanoparticles interact with cells in the physiological environment. This study evaluated the two-way interaction between inorganic nanomaterials (INMs) and cells from A549 human lung carcinoma cell line. The interaction between silica and zinc oxide INMs and cells was investigated using both standard methods and advanced characterization techniques. The effect of INMs on cell properties was evaluated in terms of cell viability, chemical modifications, and volume changes. The effect of cells and culture medium on INMs was evaluated using dynamic light scattering (DLS), scanning electron microscopy and energy-dispersive X-ray spectroscopy (SEM-EDS), high performance liquid chromatography (HPLC), gas chromatography-mass spectroscopy (GC-MS), Fourier transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA). No cytotoxic effect was detected in the case of silicon oxide INMs, while for high doses of zinc oxide INMs a reduction of cell survival was observed. Also, increased cell volume was recorded after 24 h incubation of cells with zinc oxide INMs. A better dimensional homogeneity and colloidal stability was observed by DLS for silicon oxide INMs than for zinc oxide INMs. SEM-EDS analysis showed the effectiveness of the adopted dispersion procedure and confirmed in the case of zinc oxide INMs the presence of residual substances derived from organosilane coating. HPLC and GC-MS performed on INMs aqueous dispersions after 24 h incubation showed an additional peak related to the presence of an organic contaminant only in the case of zinc oxide INMs. FTIR Chemical Imaging carried out directly on the cells showed, in case of incubation with zinc oxide INMs, a modification of the spectra in correspondence of phospholipids, nucleic acids and proteins characteristic absorption bands when compared with untreated cells. Overall, our results confirm the importance of developing new experimental methods and techniques for improving the knowledge about the biosafety of nanomaterials.