The Dubois Collection at Naturalis Biodiversity Center has a complicated past. It is a paleoanthropological and paleontological collection of great scientific value, particularly the well-known ‘Java Man’ fossils. There is also increasing awareness of its colonial context and the cultural and historical meaning of this collection that has been contested since Indonesian independence and affecting bilateral relations. The history of the collection also reveals an imbalance in opportunity to study the collection and associated archives. In this project, we create 1) a theoretical framework for colonial palaeoanthropology collections globally (i.e. collections with early human remains) , applied to the ‘Java Man’ case study, and 2) a new hypothesis on the scientific meaning of these fossils that together produce working knowledge on the contents and meaning of the Dubois Collection and the ‘Java Man’ fossils. The theoretical framework and working knowledge further mutual understanding between stakeholders and provide input for future restitution requests, decreasing tensions surrounding them, and help maintaining good cooperation. In doing so, the ‘Many Faces of Java Man’ project will also provide input for museum exhibitions and media outreach that create awareness in the Netherlands and in Indonesia on a) the relationship between colonial history and palaeoanthropological collections, b) the multifaceted meaning of such collections, and c) their scientific potential, thereby inspiring new narratives in the future. Investments in knowledge, expertise, and infrastructure will stimulate the fields of palaeoanthropology and history of science in Indonesia, not only with regards to the Dubois Collection and Java Man fossils, but also structurally, thereby furthering academic equity.