Recent experiments have reported an opposite sign of the differential surface stress produced on gold-coated cantilevers by a thiol-derivatized single-stranded DNA (SH-DNA) immobilization process. The sign of the surface stress depends on the method used to evaporate the gold thin film, being compressive (negative) or tensile (positive) for e-beam or resistively deposited gold, respectively. This study investigates the origin of this effect by means of a combination of x-ray diffraction and x-ray photoelectron spectroscopy. Both e-beam and resistively grown gold thin films are characterized to find the subtle differences responsible for this intriguing stress behaviour. Somewhat remarkably, these studies show a tight relation between the surface structure of the gold overlayer and the SH-DNA immobilization efficiency. The average grain size variation seems to correlate well with the differential surface stress triggered by the SH-DNA immobilization previously reported. These results suggest that the relation of the probe molecules with the surface structure must be considered to understand surface stress changes.