Bare rock surfaces in dry to semiarid places of the world often host a black-brown accretion rich in Mn and Fe known as rock varnish. The varnish surface presents an ideal environment for microbial development. A burgeoning interdisciplinary arena of scholarship focuses on the biogeochemical fingerprints of life in severe settings. Given that a large number of researchers hypothesize that varnish formation is a key process by microorganisms, the high altitude Ladakh remains a largely unexplored research setting. Thus, as one of the world’s harshest dry deserts, we selected Ladakh as the focus for this investigation into the nature of organic biomarkers found in subaerial rock varnish in this severe climate. Microbial fingerprinting using organic biomarkers and isotopic analyses in conjunction with electron microscopy reveals the presence of organic metabolites such as fatty acids, alkyl benzenes, oxime, amide, and fatty acids that we interpret as resulting from mineral–microbial interactions. We hypothesize that a newly discovered change in surface wettability characteristics from hydrophilic (in host rock) to hydrophobic (in varnish) might be important in facilitating the development of microbial processes that could be related to varnish formation.