Synchrotron X-ray scattering measurements were used to assess the interaction of silica nanotubes (SNTs) with membrane model systems in conditions that mimic the physiological pH of healthy (pH 7.4) and pathological (pH 5.0) cellular membranes. SNT arrays were synthesized combining the sol–gel method with a porous anodic alumina (PAA) template assisted approach. The inner surfaces of the SNTs were functionalized with aminopropylethoxysilane (APTES). Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to characterize the nanocarriers. A therapeutic anti-inflammatory drug (naproxen) was loaded into the SNTs by electrostatic interactions between the negatively charged carboxyl group of the drug and the protonated inner surface of the nanotubes. Small angle X-ray scattering (SAXS) measurements indicate that the unloaded SNTs do not interact significantly with both membranes. The negligible membrane disordering effect demonstrated by the unloaded SNTs may correlate with a desirable lack of membrane toxicity of these nanocarriers. Furthermore, the biophysical effect on membrane structure presented a similar profile at pH 5.0 for the drug (non-encapsulated) and for SNTs loaded with the drug indicating that SNTs are able to release the drug content under pathological conditions.