Historians of science have recently become increasingly involved with collections and scientific instruments. This creates opportunities for a more significant role of history in museums of science, as well as more meaningful and contextualized exhibitions and educational programmes. However, complementing the mainstream focus on universal scientific principles with history requires structural and cultural changes in museums' approaches and practices. In this paper we draw from recent collaborative work with historians of science at the University of Lisbon to reflect on the challenges museums face as they prepare for a more meaningful historical approach to science. We argue that documentation is crucial both before objects enter the museum and as regular collections practice. We propose a conceptual and methodological framework comprising two operational levels: documenting individual objects and documenting collections.