The Atacama Desert frequently serves as model system for tracing life under extremely dry conditions. We hypothesized that traces of life in the Atacama Desert follow distinct micro- and macro-scale gradients such as soil depth and elevation, respectively. Different depth intervals of surface soils (0–1, 1–5, and 5–10 cm) were sampled at five sites along an elevational transect near the Quebrada Aroma, spanning from the hyperarid core of the desert towards the arid Western Andean Precordillera (1300 to 2700 m a.s.l.), and from one additional site in the hyperarid core near Yungay. We determined the contents of major elements, pedogenic minerals and oxides, organic carbon (OC), and its δ13C and δ15N isotopic composition. The presence of living microorganisms was assessed by cultivation, and bacterial community composition was analyzed based on 16S rRNA gene sequencing. Additional information about past and present plant and microbial life was obtained from lipid biomarker analysis. We did not detect consistent micro-scale distributions for most of these proxies within the soils. However, concentrations of OC and of long-chain, plant wax-derived n-alkanes increased in soils along the aridity gradient towards the wetter sites, indicating the presence of past life at places presently not covered by vegetation. Likewise, bacterial abundance and diversity decreased as hyperaridity increased and the microbial community composition changed along the transect, becoming enriched in Actinobacteria. The distributional patterns of phospholipid fatty acids (PLFAs) confirmed the larger bacterial diversity at the higher, more humid sites compared to the drier ones. Archaeal isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) and bacterial branched (br)GDGTs, which can also indicate past life, did not follow a clear elevational trend and were absent at the driest site. Taken together, plant-derived and microbiological markers follow primarily the macro-scaled elevation and aridity gradient. Viable bacteria are present even at the driest sites, while detected biomolecules also indicate past life. The detection of past plant life in nowadays apparently lifeless regions suggests that conditions for life were less hostile in former times.