Jebel Moya is a geological granite outcrop that breaks through the sandstone formation of the Gezira Plain. Its importance to the Neolithic pastoralists who eventually built the cemetery is not mysterious. The Gezira plain has no permanent surface water, which is a problem if you keep cattle. But the Basement Complex beneath the sandstone contains an aquifer replenished by both the Blue and White Niles, and where outcrops like Jebel Moya break the surface, the aquifer's water rises within reach. The jebel was, in other words, a reliable well in a plain that otherwise did not offer one. The ecological conditions for pastoralism held here from about 1000 BCE to 1000 CE, and across roughly the same millennium, people kept burying their dead in the stones around the rising water.

Sir Henry Wellcome, the pharmaceutical magnate with an archaeologist's compulsion, began excavating Jebel Moya in 1911 and continued until 1914. Four field seasons cleared approximately a fifth of the 10.4-hectare site. The team reported 2,883 graves, of which 2,792 were fully excavated; the rest were left undisturbed. Some graves held only pottery, no bodies. Others held multiple bodies. Twenty-five contained animal burials. In total 3,137 individuals were recovered. After Wellcome's death and the interruption of the Second World War, the osteological analysis fell to J.C. Trevor at Cambridge, who worked with R. Mukherjee and C.R. Rao. Their 1955 report was groundbreaking for applying Mahalanobis D2 distance to craniometric data, allowing the Jebel Moya population to be compared with nineteen other African samples. The result marked Jebel Moya as biologically distinct but fitting within a broader northeast African pattern.

New excavations began in 2017 under University College London and the University of Khartoum. They have found that occupation of the site was more continuous than the earlier phase-based picture suggested. Archaeobotanical analysis produced the most surprising result. Domesticated sorghum, Sorghum bicolor, was radiocarbon dated at Jebel Moya to between 2550 and 2210 BC. That is roughly a thousand years earlier than the previous consensus for domesticated sorghum in this region. Sorghum is an African domesticate, not a Southwest Asian one, and finding it this early at Jebel Moya reshapes how researchers think about the timing and geography of African agricultural origins. The other definite food plant found at Jebel Moya was jujube, a savanna shrub, a reminder that these people ate across a gradient of wild and cultivated resources.

In 1999 Rachel Hutton MacDonald completed a dental anthropological study that drew striking conclusions about the Jebel Moya population. Dental caries, which form when mouth pH drops below 5.5, affected only 0.2 percent of the 2,411 teeth examined, a rate consistent with known pastoral societies and far below the 15.1 percent seen in the Meroitic Nubian population. The caries at Jebel Moya most often occurred on the third molar, matching the pastoralist pattern rather than the agricultural one, which would have concentrated damage on the second molar. Dental macrowear followed the pastoralist profile too: oblique wear angles and cupped forms, with molars worn before incisors. Enamel chipping was common, possibly from diet, possibly from using teeth as tools, and affected men and women equally. The ritual removal of incisors and canines was the culture's clearest dental signature.

All surviving site features, including the graves, date to Phase II (roughly 3000-800 BCE) and Phase III (800-100 BCE). After that the cemetery falls quiet. Why Jebel Moya was abandoned is still open. The archaeologist M. Brass has suggested that the spread of Christianity across the southern Gezira during the 600s CE may have altered trade and social networks enough to make the old gathering place no longer central. The shift from sorghum and cattle to new economic and religious systems could have pulled people elsewhere. What remains is the stone outcrop, the water below it, the thousands of burials, and the teeth, carefully removed in life and carefully analyzed long after the lives ended. Three thousand individuals from one hillside is a lot of people to have lived, herded, pulled each other's teeth, and buried each other here.