Studies of hyper-arid sites contribute to our understanding on how life adapted to extreme conditions. They are often used to further deduce implications for extraterrestrial biology by the so-called analogue site-approach. The Atacama Desert, Chile, is one of the most prominent analogue sites despite its neighboring productive ecosystems due to its hyper-aridity and geochemical features resembling Martian environments. We hypothesize that many drivers of extremophile life in analogue sites are only mistakenly attributed to aridity alone, thus obscuring a clear view of the far more complex process interactions originating in nearby earthly ecosystems. To test this, we investigated 54 soil profiles up to 60 cm of soil depth along of four transects in the Atacama Desert, either running parallel (S-N) or perpendicular (W-E) to the Andes. Our objective was to reveal the processes controlling the formation of soil organic carbon (SOC) as the most reliable proxy for microbial life in order to understand the boundary conditions of life in extreme habitats. Further, we aimed at identifying analogue sites as uncompromised as possible by external influences of for example, vegetated or marine ecosystems. We found a mixture of influences driving habitable conditions on gradients perpendicular to the Andes, for example, fog and precipitation scavenging caused by altitudinal variations and differing proximity to the Pacific Ocean, while transects parallel to the Andes were much less biased by external factors. Our results show that studies on life under extreme conditions should clarify the explanatory strength of the investigated factors by a gradient study approach.