Human settlement activities have caused changes in soil chemical properties that might remain preserved in the soil archive for a very long time. These traces might be close to irreversible on the timescale of known civilizations. Our study explores the potential of an extensive mapping of the multi-elemental composition of soil and buried sediments by a portable XRF spectrometer, using the Tel Burna site in the southern Levant as a case study. The tell, dating from the 3rd to the 1st millennium BCE, is known as a Bronze Age Canaanite settlement, and later in the Iron Age as a stronghold on the historic border between the Kingdom of Judah and Philistia. We compared the results of our geochemical survey conducted on the surface layer of contemporary soil with the data acquired by the same method from the archaeological stratigraphy exposed during excavations of the site. We found that handheld XRF spectrometry can reveal archaeologically meaningful patterns of the multi-elemental composition of soils and sediments in the horizontal plane, as well as in vertical profiles. Such patterns correspond to areas and loci of ancient settlement activities, dated to millennia ago. This methodology, if used critically, provides a rapid and cost-effective analysis of soil chemical composition that can significantly enhance our understanding of archaeological sites in arid environments.