Geoarchaeological survey on the island of Gozo combined with test excavations and new chronometric dating of two Neolithic temple sites at Santa Verna and Ġgantija on the Xagħra plateau have revealed well-preserved buried soils which tell a new story of soil development and change for the early-mid-Holocene period. Micromorphological analysis has suggested that the earlier Neolithic climax soil type was a thick, well-developed, humic and clay-enriched argillic brown Mediterranean soil. With human intervention on the Xagħra Upper Coralline Limestone plateau from at least the early 4th millennium BCE, the trajectory of soil development quickly changed. Radical soil change was marked by the removal of scrub woodland, then consequent poorer organic status and soil thinning, and rubefication and calcification, no doubt exacerbated by Neolithic agricultural activities and a more general longer-term aridification trend. The beginnings of this transitional brown to red Mediterranean soil change process has been observed at Santa Verna temple by the early 4th millennium BCE, and appears to be much further advanced by the time of the latter use of Ġgantija temple in the early-mid-3rd millennium BCE. There is also evidence of attempts at amending these deteriorating soils during this period and into the 2nd millennium BCE, a practice which probably underpinned the viability of later Neolithic agricultural society in the Maltese Islands. The changes observed ultimately resulted in the creation of the thin, xeric, red Mediterranean soils on the Coralline Limestone mesa plateaux which are typical of much of Gozo and Malta today.