When Belgian archaeologist Francis Van Noten led a joint expedition to Matupi Cave in 1973-74, working with the Institut des Musees Nationaux du Zaire and the Royal Museum for Central Africa in Tervuren, his team excavated ten square meters of deposit in meticulous five-centimeter spits. What they found was a stratigraphic record of human presence stretching from the Iron Age down through more than two meters of Late Stone Age material. The cave itself is modest in size, roughly seven meters high, eight meters deep, and five meters wide, but its proportions made it ideal for habitation. In a single grid square alone, archaeologists recovered 8,045 microlithic artifacts, of which 824 showed traces of use as tools. Nearly all were fashioned from milky vein quartz, with only about four percent made from other stone types like quartzite, flint, or sandstone.

The middle layers of the excavation, between 65 and 140 centimeters deep, yielded the richest concentration of artifacts, along with something more evocative: concentrations of burnt soil, charcoal, and small scorched quartzite pebbles that mark the locations of ancient hearths. Someone built fires here repeatedly, over centuries or millennia, in a living space defined by an irregular stone wall that separated the lit entrance area from a darker corridor leading into the cave's interior. The hearths clustered on the daylight side of this wall, suggesting a domestic arrangement that any modern camper would recognize. The most common tools were scrapers, borers, and burins, and the high proportion of woodworking implements points to an entire material culture made from perishable wood that has long since vanished, possibly including projectile weapons.

The faunal remains in Matupi Cave arrived in fragments so small that 90 percent measured less than 2.5 centimeters, and only about eight percent could be securely identified. Wim Van Neer of the Royal Museum for Central Africa spent years analyzing them, piecing together a picture of what the cave's inhabitants ate. The identifiable bones came from duikers and other small antelopes, wild pigs, fruit bats, and rodents. Sporadic remains of birds, reptiles, fish, and mollusks had almost certainly been carried in by human hands rather than natural processes. But the bones revealed something beyond diet. In the upper layers, forest-dwelling animals predominated. Deeper down, their place was taken by creatures of open savanna. The transition records a profound environmental shift: sometime between 12,000 and 3,000 years ago, the landscape around Matupi Cave changed from grassland or gallery-forest into the dense tropical forest that stands there today.

Carbon-14 dating confirmed what the stratigraphy suggested. The deepest artifacts date to more than 40,000 years before present, making the microliths found at that level among the oldest Late Stone Age tools in Africa. This discovery forced a rethinking of terminology: the presence of Late Stone Age materials in every excavated layer, from the deepest to the most recent, proved that the term describes a technology, not a time period. People at Matupi Cave were making the same fundamental type of tiny, precise stone tools for tens of thousands of years, adapting the technique to changing environments and needs. Curiously, the upper layers also contained an abundance of fruit bat remains showing no signs of having been eaten, alongside fewer human artifacts. The bats had apparently reclaimed the cave during periods when people abandoned it, only to be displaced again when humans returned. Matupi Cave was not continuously occupied. It was returned to, again and again, across a span of time that dwarfs recorded history.