Desert varnish is a dark microlayer that forms on rocky surfaces that is usually associated with arid and desert environments. It consists mainly of clay minerals (60%), while the rest are Fe and Mn oxides. Growth rates are very slow and vary from <1 to 40 mu m/ky. Although different proposals exist to explain their formation mechanisms, these processes are still unknown. Around the world, various groups and human communities have created petroglyphs with different meanings in desert varnish. In the Sonoran Desert, the archaeological site La Proveedora is known for having many petroglyphs made in granite rock varnishes. It is believed that people groups occupied the area during the mid-Holocene (ca 5000-3000 BC). The research was carried out by analyzing and looking for possible signals and contributions from past environments and current processes that are preserved in the varnish layers. The X-ray diffraction, laser breakdown spectra and scanning electron microscopy with energy dispersive spectroscopy analyses in varnish samples, showed that the distribution and concentrations of Fe and Mn exhibit an alternating behavior on a depth scale from the surface until contact with granite. The DNA analysis showed a major presence of the Proteobacteria and Actinobacteria groups. Notably, some of these microorganisms can incorporate Fe and Mn into their metabolic processes and mobilize them through the varnish for its formation. The C-14 radiocarbon dating (370 +/- 54 cal BP) indicates a very young age associated primarily with recent microorganisms. However, a first approximation was obtained for the minimum age (50001000 yr BP). The comparison between the areas of varnish and the surfaces within the petroglyphs suggests that the varnish formation occurred under conditions in the past when the humidity was higher, and that it is probably a very slow, intermittent or uncoated formation mechanism today.