Using fluorescence spectroscopy techniques, the interaction of pyrenyl-1-carboxylic acid with diphenylalanine nanotubes and the effect of pH on the assembled nanostructures were studied. The nanotubes were doped with the fluorophore, and it was found that the fluorophore concentration affected the final structures. The nanotubes obtained at low pH are smaller than those obtained at neutral pH. The nanotubes self-arrange to produce microribbons at high pH values, and this behavior is quite distinct at high fluorophore concentrations, as shown by scanning electron microscopy (SEM), epifluorescence microscopy (EPM), and X-ray diffraction (XRD) measurements. These materials were placed onto glass and glass-modified ITO, and fluorescence spectroscopy data show that the ITO interacts with the nanotubes and that a radioactive energy-transfer process between pyrenyl moieties and ITO is favored. To gain insight into the interactions between nanotubes and pyrenyl at the molecular level, molecular dynamics simulations were carried out. The computational results show that the fluorophore doping absorbs strongly at the tube surface. Thus, surface functionalization of the nanotube was observed. The pyrenyl apolar group interacts with the tube, and its polar head is exposed to interactions with water molecules in the medium.