Microarchaeological methods, especially those focused on geoarchaeology and radiocarbon dating, have revolutionized the manner in which the Iron Age settlement peak in the Negev Highlands is interpreted. We review here results from field and laboratory studies conducted at two Iron Age sites (Atar Haroa and Nahal Boqer) compared to one Byzantine/Early Islamic site (Wadi el-Mustayer)—all located near Sede Boqer. We present our methodology, which is based on small-scale but detailed excavations, study of sediments, and identification of livestock dung remains and their utility as indicators of past subsistence practices. To this we add meticulous 14C dating, ceramic petrography, and identification of botanic and zoological remains. We conclude that subsistence during the Iron Age included tending livestock but did not include agriculture. We further propose that the long-distance trade of copper from the Arabah Valley under Egyptian auspices and possibly the trading of cinnamon, dates, and other Arabian/Indian commodities were the driving force in the initiation (and later decline) of the Iron Age settlement system. We hypothesize that the agricultural settlement peak during the Byzantine/Early Islamic period was also influenced by an imperial power from outside of the Negev and that large-scale agriculture was enabled due to the adoption of new agricultural techniques, including terracing of ephemeral streams along with water diversion systems and possibly water storage facilities such as advanced cisterns. Future studies are expected to shed additional light on the complexity of settlement oscillations in the Negev Highlands region in key periods such as the Early and Intermediate Bronze Ages.