Magnetic polarity stratigraphy and magnetic palaeointensity stratigraphy is often used on sedimentary rocks to correlate outcrops and establish chronologies. The concept is based on the assumption that dipolar geomagnetic variations are globally synchronous and independent of climate and depositional conditions. The strengths of the method include the wide dating range and the applicability to a large variety of sediments and rocks. Best results are gained if long continuous sequences with high and uniform sedimentation rates are available. In the Atacama Desert, however, these perfect conditions are rare, as the landscape is strongly influenced by tectonic processes and extreme climatic conditions. Within the CRC1211 “Earth Evolution at the Dry Limit” magnetic stratigraphy is used to improve the age control of long drill cores from the claypans PAG, Huara, and Paranal, and of discrete samples from the marine Bahia Inglesia Formation. In addition, a first methodological attempt is being made to validate the potential of gypsum wedges as possible palaeomagnetic archive. The analyses are particularly carried out in order to specify the time covered by these geoarchives. Challenges for the palaeomagnetic analysis of the different archives arise from the often quite brittle nature of the unconsolidated sediments, the weak magnetizations and the complex magnetic mineralogy, potentially biased by diagenesis. Here we present challenges of the ongoing studies, as well as first results and perspectives.