Enkapune Ya Muto sits on the Mau Escarpment above the Naivasha basin in the Central Rift Valley. The area is rich in volcanic geological features, and obsidian, the dark volcanic glass that ancient toolmakers prized for its razor-sharp edges, is abundant. Archaeologist Stanley Ambrose first excavated the site in 1982, uncovering artifacts from both the Middle Stone Age and Later Stone Age. He returned in 1987 for a larger excavation covering 10 square meters, digging to a depth of 5.54 meters to recover Late Pleistocene data and pin down the transition from Middle to Late Stone Age technologies. In total, 18 one-meter squares in the northern section of the rock shelter were excavated. Ambrose's work revealed 18 main strata, each dated through radiocarbon analysis, though some dates carry uncertainty due to small sample sizes or contamination from long storage.

The discovery that made Enkapune Ya Muto internationally significant lies in a layer called DBL, attributed to the Late Stone Age Sakutiek Industry. This stratum contained approximately 69,000 pieces of flaked stone, mostly convex end scrapers and backed microliths, alongside some Middle Stone Age tools such as small bifacially flaked knives and discoidal cores. But the beads are what matter most. Thirteen complete ostrich eggshell beads, 12 preforms showing the manufacturing process, and 593 shell fragments were recovered. Charcoal from the layer dated to about 35,800 years before present, and the ostrich eggshells themselves to 39,900 years before present. The sheer quantity of manufacturing debris suggests not a casual activity but a sustained one, carried out during a period of high occupation. These beads are evidence that symbolic behavior, the impulse to mark identity and create beauty, was well established among humans in East Africa tens of thousands of years before the first cities.

Reading the stratigraphy of Enkapune Ya Muto is like reading a compressed autobiography of human development in East Africa. The deepest excavated layers contain Middle Stone Age Endingi Industry tools alongside the bones of hartebeest, zebra, and eland. Above those, the Nasampolai Industry layers show obsidian blades with red ochre staining, their edges suggesting a long period of abandonment before 40,000 years ago. Then come the Sakutiek layers with their bead workshops. Higher still, Eburran Phase 4 strata from the early Holocene record a landscape in transition: cheetah and warthog remains appear, signaling the retreat of montane forest and the spread of open grassland. The first domesticated goats and sheep arrive around 4,000 years before present. The first pottery appears at roughly the same time. Cattle show up somewhat later. By the Elmenteitan period, obsidian tools and well-preserved stained bone fill the layers, and by the Iron Age, Lanet Tradition pottery marks the final cultural transition preserved in the shelter's sediments.

Faunal remains at Enkapune Ya Muto do more than catalog the animals that once lived nearby. They record climate change. In the deeper Eburran Phase 4 layers, the presence of golden jackal suggests low-altitude savanna surrounding the site, while Curtis Marean noted that the retreat of Lake Naivasha during this period likely created short-grass habitats. Higher in the sequence, as the Holocene drying trend intensified, wild fauna diversity shifted. The appearance of mountain reedbuck replacing bohor reedbuck as the dominant species indicates environmental change on the escarpment itself. By the time the first domestic caprines appear around 4,000 years ago, the faunal record shows a community in transition: people supplementing wild game with managed herds, then gradually depending on them. The pattern of animal bone ages also tells a story. In the Eburran Phase 5 layers, most domestic animals were culled at around 20 months, while in the later Elmenteitan period, animals survived longer before slaughter, suggesting different herding strategies across cultures sharing the same shelter.