Gishimangeda Cave, near Lake Eyasi in northern Tanzania, exemplifies many challenges inherent in studying poorly documented “legacy collections” in African archaeology. The archaeological assemblage of at least twelve human individuals and associated artifacts was excavated in 1967 for primarily physical anthropological purposes. However, it has been difficult to link the materials to archaeological contexts or chronology. Recently, ancient DNA analysis of eleven individuals, eight of whom yielded direct dates of the later third millennium and early second millennium BP, has reinvigorated interest in what the site can reveal about social processes during the Pastoral Neolithic era (~5000–1200 years before present) and the transition to food production in eastern Africa. Here, we present an in-depth investigation of the history of research and excavation, and we provide descriptions of the human skeletal remains and material culture at Gishimangeda Cave and their archaeological contexts reconstructed using archival documents and photographs. Osteological analyses reveal individuals’ lived experiences and health. Three individuals have bilateral lesions on their petrous pyramids consistent with chronic otitis media, a condition that has yet to be archaeologically documented in eastern Africa. Through the analysis of the artifacts, we establish connections between Gishimangeda Cave and broadly contemporaneous herder and forager communities in the Lake Eyasi Basin. This case study illustrates the challenges and potential benefits of working with legacy collections in African archaeology. The article contributes to wider discussions in archaeology and museum studies about museum collections and the evolving ethical and scholarly obligations to them.