The Atacama Desert, despite its extreme hostile conditions, still harbours traces of life in its dusty surface. Until now, it remains open whether organic molecules found in topsoils have their origin from in-situ biotic processes in the hyper-arid core, or whether and to which degree they stem from outside the desert and its border regions. In order to trace atmospheric organic matter input, we analyzed the concentration of polycyclic aromatic hydrocarbons (PAHs) which almost exclusively derive from combustion processes and compared this to total organic carbon (TOC) concentrations. We sampled topsoil (0–15 cm depth) in one coastal (Paposo) and one inland aridity transect (Aroma) and compared them to atmospheric dust collected over two months in the hyper-arid core of the desert (Yungay). We found TOC and PAHs in all desert soil and dust samples. The sum of 18 analyzed PAHs ranged from 0.001 to 0.31 ng g−1 in the Paposo transect and from 0.14 to 0.78 ng g−1 in the Aroma transect, with moderate correlation (R2 = 0.68, p < 0.05) between TOC and PAHs. Measured PAH concentration in the dust was up to 5000 times higher and varied between 0.45 and 5.31 ng g−1. PAHs contributed with up to 0.25% to the TOC in dust and with 0.1% to the TOC in soils. This indicates that not all organic matter found in deserts is a trace for life defying extreme conditions, as it can also stem from sources outside or at the borders of the desert. We hence recommend verifying the origin of organic matter found in regions at the dry limit and highlight the overall presence of atmospheric pollutants on earth.