SiOx films were deposited using an atmospheric-pressure transporting discharge, and we adopted tetraethyl orthosilicate (TEOS) as the precursor. We studied the effects of nozzle-substrate distance, applied power, deposition time, and precursor inlet positions on the substrates placed at the tube exit. The deposited thin films were investigated using field-emission scanning electron microscopy and attenuated total-reflection Fourier-transform infrared spectroscopy. The specific studies that we carried out showed a clear relationship between the operating parameters of the deposition process and the morphological and chemical properties of the deposited films. In addition to samples treated outside of the tube in the jet mode, transporting discharge was used to deposit SiOx thin films inside fluorinated ethylene propylene (FEP) tubes. Changing the chemistry inside the FEP tubes completely modified the interaction of CT-26 cells; that is, the nonadhesive FEP tubes became completely adhesive. This study shows the potential for modifying surfaces properties inside tubes for different biological applications.